Analysis of nucleic acid sequences

ABSTRACT

The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.

CROSS-REFERENCE

This application is a continuation of U.S. patent application Ser. No.14/752,589, filed Jun. 26, 2015, which claims priority to U.S.Provisional Patent Application No. 62/017,808, filed Jun. 26, 2014, andU.S. Provisional Patent Application No. 62/072,214, filed Oct. 29, 2014,each of which applications are herein incorporated by reference in theirentirety for all purposes.

BACKGROUND

A fundamental understanding of a particular human genome may requiremore than simply identifying the presence or absence of certain geneticvariations such as mutations. It is also important to determine whethercertain genetic variations appear on the same or different chromosomes(also known as phasing). Information about patterns of geneticvariations, such as haplotypes is also important, as is informationabout the number of copies of genes.

The term “haplotype” refers to sets of DNA sequence variants (alleles)that are inherited together in contiguous blocks. In general, the humangenome contains two copies of each gene—a maternal copy and a paternalcopy. For a pair of genes each having two possible alleles, for examplegene alleles “A” and “a”, and gene alleles “B” and “b”, the genome of agiven individual will include one of two haplotypes, “AB/ab”, where theA and B alleles reside on the same chromosome (the “cis” configuration),or “Ab/aB, where the A and B alleles reside on different chromosomes(the “trans” configuration). Phasing methods or assays can be used todetermine whether a specified set of alleles reside on the same ordifferent chromosomes. In some cases, several linked alleles that definea haplotype may correlate with, or be associated with, a particulardisease phenotype; in such cases, a haplotype, rather than any oneparticular genetic variant, may be the most determinative factor as towhether a patient will display the disease.

Gene copy number also plays a role in some disease phenotypes. Mostgenes are normally present in two copies, however, amplified genes aregenes that are present in more than two functional copies. In someinstances, genes may also undergo a loss of functional copies. A loss orgain in gene copy number can lead to the production of abnormal levelsof mRNA and protein expression, potentially leading to a cancerous stateor other disorder. Cancer and other genetic disorders are oftencorrelated with abnormal (increased or decreased) chromosome numbers(“aneuploidy”). Cytogenetic techniques such as fluorescence in situhybridization or comparative genomic hybridization can be used to detectthe presence of abnormal gene or chromosome copy numbers. Improvedmethods of detecting genetic phasing information, haplotypes or copynumber variations are needed in the art.

SUMMARY

The present disclosure provides methods and systems that may be usefulin providing significant advances in the characterization of geneticmaterial. These methods and systems can be useful in providing geneticcharacterizations that may be substantially difficult using generallyavailable technologies, including, for example, haplotype phasing,identifying structural variations, e.g., deletions, duplications,copy-number variants, insertions, inversions, translocations, longtandem repeats (LTRs), short tandem repeats (STRs), and a variety ofother useful characterizations.

An aspect of the disclosure provides a method for identifying one ormore variations in a nucleic acid, comprising: a) providing a firstfragment of the nucleic acid, wherein the first fragment has a lengthgreater than 10 kilobases (kb); (b) sequencing a plurality of secondfragments of the first fragment to provide a plurality of fragmentsequences, which plurality of fragment sequences share a common barcodesequence; (c) attributing the plurality of fragment sequences to thefirst fragment by a presence of the common barcode sequence; (d)determining a nucleic acid sequence of the first fragment using theplurality of fragment sequences, wherein the nucleic acid sequence isdetermined at an error rate of less than 1%; and; (e) identifying theone or more variations in the nucleic acid sequence of the firstfragment determined in (d), thereby identifying the one or morevariations within the nucleic acid.

In some cases, the first fragment is in a discrete partition in among aplurality of discrete partitions. In some cases, the discrete partitionis a droplet in an emulsion. In some cases the identifying comprisesidentifying phased variants in the nucleic acid sequence of the firstfragment. In some cases, the identifying comprises identifying one ormore structural variations in the nucleic acid from the nucleic acidsequence of the first fragment. In some cases, the first fragment has alength greater than 15 kb. In some cases, the first fragment has alength greater than 20 kb. In some cases, the determining comprisesmapping the plurality of fragment sequences to a reference. In somecases, the determining comprises assembling the plurality of fragmentsequences with the common barcode sequence.

In some cases, the method for identifying one or more variations furthercomprises providing a plurality of first fragments of the nucleic acidthat are at least 10 kb in length, and the identifying comprisesdetermining a nucleic acid sequence from each of the plurality of firstfragments and identifying the one or more variations in the nucleic acidfrom the nucleic acid sequence from each of the plurality of firstfragments.

In some cases, the method for identifying one or more variations furthercomprises linking two or more nucleic acid sequences of the plurality offirst fragments in an inferred contig based upon overlapping nucleicacid sequences of the two or more nucleic acid sequences, wherein themaximum inferred contig length is at least 10 kb. In some cases, themaximum inferred contig length is at least 20 kb. In some cases, themaximum inferred contig length is at least 40 kb. In some cases, themaximum inferred contig length is at least 50 kb. In some cases, themaximum inferred contig length is at least 100 kb. In some cases, themaximum inferred contig length is at least 200 kb. In some cases, themaximum inferred contig length is at least 500 kb. In some cases, themaximum inferred contig length is at least 750 kb. In some cases, themaximum inferred contig length is at least 1 megabase (Mb). In somecases, the maximum inferred contig length is at least 1.75 Mb. In somecases, the maximum inferred contig length is at least 2.5 Mb.

In some cases, the method for identifying one or more variations furthercomprises linking two or more nucleic acid sequences of the plurality offirst fragments in a phase block based upon overlapping phased variantswithin the two or more nucleic acid sequences of the plurality of firstfragments, wherein the maximum phase block length is at least 10 kb. Insome cases, the maximum phase block length is at least 20 kb. In somecases, the maximum phase block length is at least 40 kb. In some cases,the maximum phase block length is at least 50 kb. In some cases, themaximum phase block length is at least 100 kb. In some cases, themaximum phase block length is at least 200 kb. In some cases, themaximum phase block length is at least 500 kb. In some cases, themaximum phase block length is at least 750 kb. In some cases, themaximum phase block length is at least 1 Mb. In some cases, the maximumphase block length is at least 1.75 Mb. In some cases, maximum phaseblock length is at least 2.5 Mb.

In some cases, the method for identifying one or more variations furthercomprises linking two or more nucleic acid sequences of the plurality offirst fragments in an inferred contig based upon overlapping nucleicacid sequences of the two or more nucleic acid sequences, therebycreating a population of inferred contigs, wherein the N50 of thepopulation of inferred contigs is at least 10 kb. In some cases, the N50of the population of inferred contigs is at least 20 kb. In some cases,the N50 of the population of inferred contigs is at least 40 kb. In somecases, the N50 of the population of inferred contigs is at least 50 kb.In some cases, the N50 of the population of inferred contigs is at least100 kb. In some cases, the N50 of the population of inferred contigs isat least 200 kb. In some cases, the N50 of the population of inferredcontigs is at least 500 kb. In some cases, the N50 of the population ofinferred contigs is at least 750 kb. In some cases, the N50 of thepopulation of inferred contigs is at least 1 Mb. In some cases, the N50of the population of inferred contigs is at least 1.75 Mb. In somecases, the N50 of the population of inferred contigs is at least 2.5 Mb.

In some cases, the method for identifying one or more variations furthercomprises linking two or more nucleic acid sequences of the plurality offirst fragments in a phase block based upon overlapping phased variantswithin the two or more nucleic acid sequences of the plurality of firstfragments, thereby creating a population of phase blocks, wherein theN50 of the population of phase blocks is at least 10 kb. In some cases,the N50 of the population of phase blocks is at least 20 kb. In somecases, the N50 of the population of phase blocks is at least 40 kb. Insome cases, the N50 of the population of phase blocks is at least 50 kb.In some cases, the N50 of the population of phase blocks is at least 100kb. In some cases, the N50 of the population of phase blocks is at least200 kb. In some cases, the N50 of the population of phase blocks is atleast 500 kb. In some cases, the N50 of the population of phase blocksis at least 750 kb. In some cases, the N50 of the population of phaseblocks is at least 1 Mb. In some cases, the N50 of the population ofphase blocks is at least 1.75 Mb. In some cases, the N50 of thepopulation of phase blocks is at least 2.5 Mb.

An additional aspect of the disclosure provides a method of determininga presence of a structural variation of a nucleic acid. The method cancomprise: (a) providing a plurality of first fragment molecules of thenucleic acid, wherein a given first fragment molecule of the pluralityof first fragment molecules comprises the structural variation; (b)sequencing a plurality of second fragment molecules of each of theplurality of first fragment molecules to provide a plurality of fragmentsequences, wherein each of the plurality of fragment sequencescorresponding to a given first fragment molecule shares a common barcodesequence; and (c) determining the presence of the structural variationby (i) mapping the plurality of fragment sequences to a referencesequence, (ii) identifying the plurality of fragment sequences thatshare the common barcode sequence, and (iii) identifying the structuralvariation based on a presence of an elevated amount of the plurality offragment sequences sharing the common barcode sequence that map to thereference sequence at locations that are further apart than a length ofthe given first fragment molecule, which elevated amount is relative toa sequence lacking the structural variation.

In some cases, the elevated amount is 1% or more with respect to a totalnumber of the first fragment molecules that are derived from a region ofthe nucleic acid having the structural variation. In some cases, theelevated amount is 2% or more with respect to the total number of thefirst fragment molecules that are derived from a region of the nucleicacid having the structural variation. In some cases, the locations areat least about 100 bases apart. In some cases, the locations are atleast about 500 bases apart. In some cases, the locations are at leastabout 1 kilobase (kb) apart. In some cases, the locations are at leastabout 10 kb apart.

In some cases, the method of determining a presence of a structuralvariation of a nucleic acid further comprises identifying the structuralvariation by creating an assembly of the given first fragment moleculefrom the plurality of fragment sequences, wherein the plurality offragment sequences are selected as inputs for the assembly based upon apresence of the common barcode sequence. In some cases, the assembly iscreated by generating a consensus sequence from the plurality offragment sequences. In some cases, the structural variation comprises atranslocation.

An additional aspect of the disclosure provides a method ofcharacterizing a variant nucleic acid sequence. In some cases, themethod can comprise: (a) fragmenting a variant nucleic acid to provide aplurality of first fragments having a length greater than 10 kilobases(kb); (b) separating the plurality of first fragments into discretepartitions; (c) creating a plurality of second fragments from each firstfragment within its respective partition, the plurality of secondfragments having a barcode sequence attached thereto, which barcodesequence within a given partition is a common barcode sequence; (d)sequencing the plurality of second fragments and the barcode sequencesattached thereto, to provide a plurality of second fragment sequences;(e) attributing the second fragment sequences to an original firstfragment based at least in part on the presence of the common barcodesequence to provide a first fragment sequence context for the secondfragment sequences; and (f) identifying a variant portion of the variantnucleic acid from the first fragment sequence context, therebycharacterizing the variant nucleic acid sequence. In some cases, theattributing comprises assembling at least a portion of a sequence for anindividual fragment from the plurality of first fragments from theplurality of second fragment sequences based, at least in part, on thepresence of the common barcode sequence. In some cases, the attributingcomprises mapping the plurality of second fragment sequences to anindividual first fragment from the plurality of first fragments based atleast in part upon the common barcode sequence.

In some cases, the method of characterizing a variant nucleic acidsequence further comprises linking two or more of the plurality of firstfragments into an inferred contig, based upon overlapping sequencebetween the two or more of the plurality of first fragments. In somecases, the identifying comprises identifying one or more phased variantsfrom the first fragment sequence context. In some cases, the method ofcharacterizing a variant nucleic acid sequence further comprises linkingtwo or more of the plurality of first fragments into a phase block,based upon overlapping phased variants between the two or more of theplurality of first fragments. In some cases, the identifying comprisesidentifying one or more structural variations from the first fragmentsequence context. In some cases, the one or more structural variationsare independently selected from insertions, deletions, translocations,retrotransposons, inversions, and duplications. In some cases, thestructural variation comprises an insertion or a translocation, and thefirst fragment sequence context indicates a presence of the insertion ortranslocation.

An additional aspect of the disclosure provides a method of identifyingvariants in a sequence of a nucleic acid. In some cases, the methodcomprises: obtaining nucleic acid sequences of a plurality of individualfragment molecules of the nucleic acid, the nucleic acid sequences ofthe plurality of individual fragment molecules each having a length ofat least 1 kilobase (kb); linking sequences of one or more of theplurality of individual fragment molecules in one or more inferredcontigs; and identifying one or more variants from the one or moreinferred contigs. In some cases, the obtaining comprises obtaining thenucleic acid sequences of a plurality of fragment molecules that aregreater than 10 kb in length. In some cases, the obtaining comprises:providing a plurality of barcoded fragments of each individual fragmentmolecule of the plurality of individual fragment molecules, the barcodedfragments of a given individual fragment molecule having a commonbarcode; sequencing the plurality of barcoded fragments of the pluralityof individual fragment molecules, the sequencing providing a sequencingerror rate of less than 1%; and determining a sequence of the pluralityof individual fragment molecules from sequences of the plurality ofbarcoded fragments and their associated barcodes.

In some cases, the linking comprises identifying one or more overlappingsequences between two or more individual fragment molecules to link thetwo or more individual fragment molecules into the one or more inferredcontigs. In some cases, the linking comprises identifying one or morecommon variants between two or more individual fragment molecules tolink the two or more individual fragment molecules into the one or moreinferred contigs. In some cases, the one or more common variants arephased variants, and the one or more inferred contigs comprise a maximumphase block length of at least 100 kb. In some cases, the one or morevariants identified in the identifying comprise structural variations.In some cases, the structural variations are selected from insertions,deletions, translocations, retrotransposons, inversions, andduplications.

An additional aspect of the disclosure provides a method ofcharacterizing nucleic acids. In some cases, the method comprises:obtaining nucleic acid sequences of a plurality of fragment moleculeshaving a length of at least 10 kilobases (kb); identifying one or morephased variant positions in the nucleic acid sequences of the pluralityof fragment molecules; linking the nucleic acid sequences of at least afirst fragment molecule to at least a second fragment molecule basedupon a presence of one or more common phased variant positions withinthe first and second fragment molecules, to provide a phase block with amaximum phase block length of at least 10 kb; and identifying one ormore phased variants from the phase block with the maximum phase blocklength of at least 10 kb. In some cases, the method of characterizingnucleic acids further comprises identifying one or more additionalphased variants from the phase block. In some cases, the plurality offragment molecules are in discrete partitions. In some cases, thediscrete partitions are droplets in an emulsion. In some cases, thelength of the plurality of fragment molecules is at least 50 kb. In somecases, the length of the plurality of fragment molecules is at least 100kb. In some cases, the maximum phase block length is at least 50 kb. Insome cases, the maximum phase block length is at least 100 kb. In somecases, the maximum phase block length is at least 1 Mb. In some cases,the maximum phase block length is at least 2 Mb. In some cases, themaximum phase block length is at least 2.5 Mb.

An additional aspect of the disclosure provides a method comprising: (a)partitioning a first nucleic acid into a first partition, where thefirst nucleic acid comprises the target sequence derived from a firstchromosome of an organism; (b) partitioning a second nucleic acid into asecond partition, where the second nucleic acid comprises the targetsequence derived from a second chromosome of the organism; (c) in thefirst partition, attaching a first barcode sequence to fragments of thefirst nucleic acid or to copies of portions of the first nucleic acid toprovide first barcoded fragments; (d) in the second partition, attachinga second barcode sequence to fragments of the second nucleic acid or tocopies of portions of the second nucleic acid to provide second barcodedfragments, the second barcode sequence being different from the firstbarcode sequence; (e) determining the nucleic acid sequence of the firstand second barcoded fragments, and assembling a nucleic acid sequence ofthe first and second nucleic acids; and (f) comparing the nucleic acidsequence of the first and second nucleic acids to characterize the firstand second nucleic acids as deriving from first and second chromosomes,respectively. In some cases, oligonucleotides comprising the firstbarcode sequence are co-partitioned with the first nucleic acid, andoligonucleotides comprising the second barcode sequence areco-partitioned with the second nucleic acid. In some cases, theoligonucleotides comprising the first barcode sequence are releasablyattached to a first bead, and the oligonucleotides comprising the secondbarcode sequence are releasably attached to a second bead, and theco-partitioning comprises co-partitioning the first and second beadsinto the first and second partitions, respectively. In some cases, thefirst and second partitions comprise droplets in an emulsion. In somecases, the first chromosome is a paternal chromosome and the secondchromosome is a maternal chromosome. In some cases, the first chromosomeand the second chromosome are homologous chromosomes. In some cases, thefirst nucleic acid and the second nucleic acid comprise one or morevariations.

In some cases, the first and second chromosomes are derived from afetus. In some cases, the first and second nucleic acids are obtainedfrom a sample taken from a pregnant woman. In some cases, the firstchromosome is chromosome 21, 18, or 13. In some cases, the secondchromosome is chromosome 21, 18, or 13. In some cases, the methodfurther comprises determining the relative quantity of the first orsecond chromosome. In some cases, the method further comprisesdetermining the quantity of the first or second chromosome relative to areference chromosome. In some cases, the first chromosome or secondchromosome, or both, has an increase in copy number. In some cases, theincrease in copy number is a result of cancer or aneuploidy. In somecases, the first chromosome or second chromosome, or both, has adecrease in copy number. In some cases, the decrease in copy number is aresult of cancer or aneuploidy.

An additional aspect of the disclosure provides a method comprising: (a)partitioning a first nucleic acid into a first partition, where thefirst nucleic acid comprises the target sequence derived from a firstchromosome of an organism; (b) partitioning a second nucleic acid into asecond partition, where the second nucleic acid comprises the targetsequence derived from a second chromosome of the organism; (c) in thefirst partition, attaching a first barcode sequence to fragments of thefirst nucleic acid or to copies of portions of the first nucleic acid toprovide first barcoded fragments; (d) in the second partition, attachinga second barcode sequence to fragments of the second nucleic acid or tocopies of portions of the second nucleic acid to provide second barcodedfragments, the second barcode sequence being different from the firstbarcode sequence; (e) determining the nucleic acid sequence of the firstand second barcoded fragments, and assembling a nucleic acid sequence ofthe first and second nucleic acids; and (f) comparing the nucleic acidsequence of the first and second nucleic acids to identify any variationbetween the nucleic acid sequence of the first and second nucleic acids.In some cases, oligonucleotides comprising the first barcode sequenceare co-partitioned with the first nucleic acid, and oligonucleotidescomprising the second barcode sequence are co-partitioned with thesecond nucleic acid. In some cases, the oligonucleotides comprising thefirst barcode sequence are releasably attached to a first bead, and theoligonucleotides comprising the second barcode sequence are releasablyattached to a second bead, and the co-partitioning comprisesco-partitioning the first and second beads into the first and secondpartitions, respectively. In some cases, the first and second partitionscomprise droplets in an emulsion. In some cases, the first chromosome isa paternal chromosome and the second chromosome is a maternalchromosome. In some cases, first chromosome and the second chromosomeare homologous chromosomes. In some cases, the first nucleic acid andthe second nucleic acid comprise one or more variations. In some cases,the first and second chromosomes are derived from a fetus. In somecases, the first and second nucleic acids are obtained from a sampletaken from a pregnant woman. In some cases, the first chromosome ischromosome 21, 18, or 13. In some cases, the second chromosome ischromosome 21, 18, or 13. In some cases, the method further comprisesdetermining the relative quantity of the first or second chromosome. Insome cases, the method further comprises determining the quantity of thefirst or second chromosome relative to a reference chromosome. In somecases, the first chromosome or second chromosome, or both, has anincrease in copy number. In some cases, the increase in copy number is aresult of cancer or aneuploidy. In some cases, the first chromosome orsecond chromosome, or both, has a decrease in copy number. In somecases, the decrease in copy number is a result of cancer or aneuploidy.

An additional aspect of the disclosure provides a method forcharacterizing a fetal nucleic acid sequence. In some cases, the methodcomprises: (a) determining a maternal nucleic acid sequence, wherein thematernal nucleic acid is derived from a pregnant mother of a fetus, by:(i) fragmenting a maternal nucleic acid to provide a plurality of firstmaternal fragments; (ii) separating the plurality of first maternalfragments into maternal partitions; (iii) creating a plurality of secondmaternal fragments from each of the first maternal fragments withintheir respective maternal partitions, the plurality of second maternalfragments having a first barcode sequence attached thereto, whereinwithin a given maternal partition of the maternal partitions the secondmaternal fragments comprise a first common barcode sequence attachedthereto; (iv) sequencing the plurality of second maternal fragments toprovide a plurality of maternal fragment sequences; (v) attributing thematernal fragment sequences to an original first maternal fragment basedat least in part on the presence of the first common barcode sequence todetermine the maternal nucleic acid sequence; (b) determining a paternalnucleic acid sequence, wherein the paternal nucleic acid is derived froma father of the fetus, by: (i) fragmenting a paternal nucleic acid toprovide a plurality of first paternal fragments; (ii) separating theplurality of first paternal fragments into paternal discrete partitions;(iii) creating a plurality of second paternal fragments from each firstpaternal fragment within its respective partition, the plurality ofsecond paternal fragments having a second barcode sequence attachedthereto, wherein within a given paternal partition, the second paternalfragments comprise a second common barcode sequence attached thereto;(iv) sequencing the plurality of second paternal fragments and thesecond barcode sequences attached thereto, to provide a plurality ofpaternal fragment sequences; (v) attributing the paternal fragmentsequences to an original first paternal fragment based at least in parton the presence of the second common barcode sequence to determine thepaternal nucleic acid sequence; (c) obtaining a fetal nucleic acid fromthe pregnant mother and determining a sequence of the fetal nucleic acidand/or one or more genetic variations of the sequence of the fetalnucleic acid using the maternal nucleic acid sequence and the paternalnucleic acid sequence.

In some cases, the paternal fragment sequences and the maternal fragmentsequences are each used to link sequences into one or more inferredcontigs. In some cases, the inferred contigs are used to constructmaternal and paternal phase blocks. In some cases, the sequence of thefetal nucleic acid is compared to the maternal and paternal phase blocksto construct fetal phase blocks. In some cases, the paternal fragmentsequences are assembled to produce at least a portion of sequences forthe plurality of first paternal fragments, thereby determining thepaternal nucleic acid sequence, and wherein the maternal fragmentsequences are assembled to produce at least a portion of sequences forthe plurality of first maternal fragments, thereby determining thematernal nucleic acid sequence. In some cases, the determining thepaternal nucleic acid sequence comprises mapping the paternal fragmentsequences to a paternal reference, and wherein the determining thematernal nucleic acid sequence comprises mapping the maternal fragmentsequences to a maternal reference.

In some cases, the sequence of the fetal nucleic acid is determined withan accuracy of at least 99%. In some cases, the one or more geneticvariations of the sequence of the fetal nucleic acid are determined withan accuracy of at least 99%. In some cases, the one or more geneticvariations are selected from the group consisting of a structuralvariation and a single nucleotide polymorphism (SNP). In some cases, theone or more genetic variations are a structural variation selected fromthe group consisting of a copy number variation, an insertion, adeletion, a translocation, a retrotransposon, an inversion, arearrangement, a repeat expansion and a duplication.

In some cases, the method for characterizing the fetal nucleic acidsequence further comprises, in (c), determining the one or more geneticvariations of the sequence of the fetal nucleic acid using one or moregenetic variations determined for the maternal nucleic acid sequence andthe paternal nucleic acid sequence. In some cases, the method forcharacterizing the fetal nucleic acid sequence further comprises, in(c), determining one or more de novo mutations of the fetal nucleicacid. In some cases, the method for characterizing the fetal nucleicacid sequence further comprises, during or after (c), determining ananeuploidy associated with the fetal nucleic acid.

In some cases, the method for characterizing the fetal nucleic acidsequence further comprises, during or after (v) in (a), haplotyping thematernal nucleic acid sequence to provide a haplotype-resolved maternalnucleic acid sequence and, during or after (v) in (b), haplotyping thepaternal nucleic acid sequence to provide a haplotype-resolved paternalnucleic acid sequence. In some cases, the method for characterizing thefetal nucleic acid sequence further comprises in (c), determining thesequence of the fetal nucleic acid and/or the one or more geneticvariations using the haplotype-resolved maternal nucleic acid sequenceand the haplotype-resolved paternal nucleic acid sequence. In somecases, one or more of the maternal nucleic acid and the paternal nucleicacid is genomic deoxyribonucleic acid (DNA). In some cases, in (c), thefetal nucleic acid comprises cell-free nucleic acid. In some cases, themethod for characterizing the fetal nucleic acid sequence furthercomprises, in (a), determining the maternal nucleic acid sequence withan accuracy of at least 99%. In some cases, the method forcharacterizing the fetal nucleic acid sequence further comprises, in(b), determining the paternal nucleic acid sequence with an accuracy ofat least 99%.

In some cases, the maternal nucleic acid sequence and/or the paternalnucleic acid sequence has a length greater than 10 kilobases (kb). Insome cases, the maternal and paternal partitions comprise droplets in anemulsion. In some cases, in (a), the first barcode sequence is providedin the given maternal partition releasably attached to a first particle.In some cases, in (b), the second barcode sequence is provided in thegiven paternal partition releasably attached to a second particle.

An additional aspect of the disclosure provides a method forcharacterizing a sample nucleic acid. In some cases, the methodcomprises: (a) obtaining a biological sample from a subject, whichbiological sample includes a cell-free sample nucleic acid; (b) in adroplet, attaching a barcode sequence to fragments of the cell-freesample nucleic acid or to copies of portions of the sample nucleic acid,to provide barcoded sample fragments; (c) determining nucleic acidsequences of the barcoded sample fragments and providing a samplenucleic acid sequence based on the nucleic acid sequences of thebarcoded sample fragments; (d) using a programmed computer processor togenerate a comparison of the sample nucleic acid sequence to a referencenucleic acid sequence, which reference nucleic acid sequence has alength greater 10 kilobases (kb) and an accuracy of at least 99%; and(e) using the comparison to identify one or more genetic variations inthe sample nucleic acid sequence, thereby associating the sample nucleicacid with a disease. In some cases, the one or more genetic variationsin the sample nucleic acid sequence are selected from the groupconsisting of a structural variation and a single nucleotidepolymorphism (SNP). In some cases, the one or more genetic variations ofthe sample nucleic acid sequence are a structural variation selectedfrom the group consisting of a copy number variation, an insertion, adeletion, a retrotransposon, a translocation, an inversion, arearrangement, a repeat expansion and a duplication. In some cases, in(c), the sample nucleic acid sequence is provided with an accuracy of atleast 99%. In some cases, in (b), the barcode sequence is provided inthe droplet releasably attached to a particle, and wherein (b) furthercomprises releasing the barcode sequence from the particle into thedroplet prior to the attaching the barcode sequence. In some cases, in(b), the barcode sequence is provided as a portion of a primer sequencereleasably attached to the particle, wherein the primer sequence alsoincludes a random N-mer sequence, and wherein (b) further comprisesreleasing the primer sequence from the particle into the droplet priorto the attaching the barcode sequence. In some cases, in (b), attachingthe barcode sequence to the fragments of the cell-free sample nucleicacid or to the copies of portions of the cell-free sample nucleic acidin an amplification reaction using the primer.

In some cases, the method for characterizing the sample nucleic acidfurther comprises: (i) in an additional droplet, attaching an additionalbarcode sequence to fragments of a reference nucleic acid or to copiesof portions of the reference nucleic acid to provide barcoded referencefragments; and (ii) determining nucleic acid sequences of the barcodedreference fragments and determining the reference nucleic acid sequencebased on the nucleic acid sequences of the barcoded reference fragments.In some cases, the determining the reference nucleic acid sequencecomprises assembling the nucleic acid sequences of the barcodedreference fragments. In some cases, the method for characterizing thesample nucleic acid further comprises providing the additional barcodesequence in the additional droplet releasably attached to a particle andreleasing the additional barcode sequence from the particle into theadditional partition prior to the attaching the additional barcodesequence. In some cases, the method for characterizing the samplenucleic acid further comprises providing the additional barcode sequenceas a portion of a primer sequence releasably attached to the particle,wherein the primer sequence also includes a random N-mer sequence, andreleasing the primer from the particle into the additional droplet priorto the attaching the additional barcode sequence. In some cases, themethod for characterizing the sample nucleic acid further comprisesattaching the additional barcode sequence to the fragments of thereference nucleic acid or to the copies of portions of the referencenucleic acid in an amplification reaction using the primer. In somecases, the method for characterizing the sample nucleic acid furthercomprises determining one or more genetic variations in the referencenucleic acid sequence.

In some cases, the one or more genetic variations in the referencenucleic acid sequence are selected from the group consisting of astructural variation and a single nucleotide polymorphism (SNP). In somecases, the one or more genetic variations in the reference nucleic acidsequence are a structural variation selected from the group consistingof a copy number variation, an insertion, a deletion, a retrotransposon,a translocation, an inversion, a rearrangement, a repeat expansion and aduplication. In some cases, the reference nucleic acid comprises agermline nucleic acid sequence. In some cases, the reference nucleicacid comprises a cancer nucleic acid sequence. In some cases, the samplenucleic acid sequence has a length of greater than 10 kb. In some cases,the reference nucleic acid is derived from a genome indicative of anabsence of a disease state. In some cases, the reference nucleic acid isa derived from a genome indicative of a disease state. In some cases,the disease state comprises cancer. In some cases, the disease statecomprises an aneuploidy. In some cases, the cell-free sample nucleicacid comprises tumor nucleic acid. In some cases, the tumor nucleic acidcomprises a circulating tumor nucleic acid.

Additional aspects and advantages of the present disclosure will becomereadily apparent to those skilled in this art from the followingdetailed description, wherein only illustrative embodiments of thepresent disclosure are shown and described. As will be realized, thepresent disclosure is capable of other and different embodiments, andits several details are capable of modifications in various obviousrespects, all without departing from the disclosure. Accordingly, thedrawings and description are to be regarded as illustrative in nature,and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference in their entiretiesto the same extent as if each individual publication, patent, or patentapplication was specifically and individually indicated to beincorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIG. 1 provides a schematic illustration of identification and analysisof phased variants using conventional processes versus example processesand systems described herein.

FIG. 2 provides a schematic illustration of the identification andanalysis of structural variations using conventional processes versusexample processes and systems described herein.

FIG. 3 illustrates an example workflow for performing an assay to detectcopy number or haplotype using methods and compositions disclosedherein.

FIG. 4 provides a schematic illustration of an example process forcombining a nucleic acid sample with beads and partitioning the nucleicacids and beads into discrete droplets

FIG. 5 provides a schematic illustration of an example process forbarcoding and amplification of chromosomal nucleic acid fragments.

FIG. 6 provides a schematic illustration of an example use of barcodingof chromosomal nucleic acid fragments in attributing sequence data toindividual chromosomes.

FIG. 7 provides a schematic illustration of an example of phasedsequencing processes.

FIG. 8 provides a schematic illustration of an example subset of thegenome of a healthy patient (top panel) and a cancer patient with a gainin haplotype copy number (central panel) or loss of haplotype copynumber (bottom panel).

FIGS. 9A-B provides: (a) a schematic illustration showing a relativecontribution of tumor DNA and (b) a representation of detecting suchcopy gains and losses by ordinary sequencing methods.

FIG. 10 provides a schematic illustration of an example of detectingcopy gains and losses using a single variant position (left panel) andcombined variant positions (right panel).

FIG. 11 provides a schematic illustration of the potential of describedmethods and systems to identify gains and losses in copy number.

FIG. 12 illustrates an example workflow for performing an aneuploidytest based on determination of chromosome number and copy numbervariation using methods and compositions described herein.

FIGS. 13A-B illustrate an example overview of a process for identifyingstructural variations such as translocations and gene fusions in geneticsamples.

FIG. 14 illustrates an example workflow for performing a cancerdiagnostic test based on determination of copy number variation usingthe methods and compositions described herein.

FIG. 15 provides a schematic illustration of an EML-4-ALK structuralvariation from an NCI-H2228 cancer cell line.

FIGS. 16A and 16B, provide barcode mapping data using the systemsdescribed herein for identifying the presence of the EML-4-ALK variantstructure shown in FIG. 15, in the cancer cell line (FIG. 16A), ascompared to a negative control cell line (FIG. 16B).

FIG. 17 schematically depicts an example workflow of analyzing apaternal nucleic acid sequence as described herein.

FIG. 18 schematically depicts an example workflow of analyzing amaternal nucleic acid sequence as described herein.

FIG. 19 schematically depicts an example workflow of analyzing a fetalnucleic acid sequence as described herein.

FIG. 20 schematically depicts an example workflow of analyzing areference nucleic acid sequence as described herein.

FIG. 21 schematically depicts an example workflow of analyzing a samplenucleic acid sequence as described herein.

FIG. 22 schematically depicts an example computer control system.

DETAILED DESCRIPTION

While various embodiments of the invention have been shown and describedherein, it will be obvious to those skilled in the art that suchembodiments are provided by way of example only. Numerous variations,changes, and substitutions may occur to those skilled in the art withoutdeparting from the invention. It should be understood that variousalternatives to the embodiments of the invention described herein may beemployed.

As used herein, the term “organism” generally refers to a contiguousliving system. Non-limiting examples of organisms includes animals(e.g., humans, other types of mammals, birds, reptiles, insects, otherexample types of animals described elsewhere herein), plants, fungi andbacterium.

As used herein, the term “contig” generally refers to a contiguousnucleic acid sequence of a given length. The contiguous sequence may bederived from an individual sequence read, including either a short orlong read sequence read, or from an assembly of sequence reads that arealigned and assembled based upon overlapping sequences within the reads,or that are defined as linked within a fragment based upon other knownlinkage data, e.g., the tagging with common barcodes as describedelsewhere herein. These overlapping sequence reads may likewise includeshort reads, e.g., less than 500 bases, e.g., in some cases fromapproximately 100 to 500 bases, and in some cases from 100 to 250 bases,or based upon longer sequence reads, e.g., greater than 500 bases, 1000bases or even greater than 10,000 bases.

I. Overview

This disclosure provides methods and systems useful in providingsignificant advances in the characterization of genetic material. Insome cases, the methods and systems can be useful in providing geneticcharacterizations that are very difficult or even impossible usinggenerally available technologies, including, for example, haplotypephasing, identifying structural variations, e.g., deletions,duplications, copy-number variants, insertions, inversions,retrotransposons. translocations, LTRs, STRs, and a variety of otheruseful characterizations.

In general, the methods and systems described herein accomplish theabove goals by providing for the sequencing of long individual nucleicacid molecules, which permit the identification and use of long rangevariant information, e.g., relating variations to different sequencesegments, including sequence segments containing other variations, thatare separated by significant distances in the originating sequence,e.g., longer than is provided by short read sequencing technologies.However, these methods and systems achieve these objectives with theadvantage of extremely low sequencing error rates of short readsequencing technologies, and far below those of the reported longread-length sequencing technologies, e.g., single molecule sequencing,such as SMRT Sequencing and nanopore sequencing technologies.

In general, the methods and systems described herein segment longnucleic acid molecules into smaller fragments that are sequenceableusing high-throughput, higher accuracy short-read sequencingtechnologies, but do such segmentation in a manner that allows thesequence information derived from the smaller fragments to be attributedto the originating longer individual nucleic acid molecules. Byattributing sequence reads to an originating longer nucleic acidmolecule, one can gain significant characterization information for thatlonger nucleic acid sequence, that one cannot generally obtain fromshort sequence reads alone. As noted, such characterization informationcan include haplotype phasing, identification of structural variations,and identifying copy number variations.

The advantages of the methods and systems described herein are describedwith respect to a number of general examples. In a first example, phasedsequence variants are identified and characterized using the methods andsystems described herein. FIG. 1 schematically illustrates thechallenges of phased variant calling and the solutions presented by themethods described herein. As shown, nucleic acids 102 and 104 in Panel Irepresent two haploid sequences of the same region of differentchromosomes, e.g., maternally and paternally inherited chromosomes. Eachsequence includes a series of variants, e.g., variants 106-114 onnucleic acid 102, and variants 116-122 on nucleic acid 104, at differentalleles that characterize each haploid sequence. Because of their veryshort sequence reads, most sequencing technologies are unable to providethe context of individual variants relative to other variants on thesame haploid sequence. Additionally, because they rely on samplepreparation techniques that do not separate individual molecularcomponents, e.g., each haploid sequence, one is unable to identify thephasing of the various variants, e.g., the haploid sequence from which avariant derives. As a result, these short read technologies are unableto resolve these variants to their originating molecules. Thedifficulties with this approach are schematically illustrated in PanelsIIa and IIIa. Briefly, pooled fragments from both haploid sequences,shown in Panel IIa, are sequenced, resulting in a large number of shortsequence reads 124, and the resulting sequence 126 is assembled (shownin Panel IIIa). As shown, because one does not have the relative phasingcontext of any of the shorter sequence reads in Panel IIa, one would beunable to resolve the variants as between two different haploidsequences in the assembly process. Accordingly, the resulting assemblyshown in Panel IIIa, results in single consensus sequence assembly 126,including all of variants 106-122.

In contrast, and as shown in Panel IIb of FIG. 1, the methods andsystems described herein breakdown or segment the longer nucleic acids102 and 104 into shorter, sequenceable fragments, as with the abovedescribed approach, but retain with those fragments the ability toattribute them to their originating molecular context. This isschematically illustrated in Panel IIb, in which different fragments aregrouped or “compartmentalized” according to their originating molecularcontext. In the context of the disclosure, this grouping can beaccomplished through one or both of physically partitioning thefragments into groups that retain the molecular context, as well astagging those fragments in order to subsequently be able to elucidatethat context.

This grouping is schematically illustrated as the allocation of theshorter sequence reads as between groups 128 and 130, representing shortsequence reads from nucleic acids 102 and 104, respectively. Because theoriginating sequence context is retained through the sequencing process,one can employ that context in resolving the original molecular context,e.g., the phasing, of the various variants 106-114 and 116-122 asbetween sequences 102 and 104, respectively.

In another exemplary advantaged application, the methods and systems areuseful in characterizing structural variants that are generallyunidentifiable or at least difficult to identify, using short readsequence technologies.

This is schematically illustrated with reference to a simpletranslocation event in FIG. 2. As shown, a genomic sample may includenucleic acids that include a translocation event, e.g., a translocationof genetic element 206 from sequence 202 to sequence 204. Suchtranslocations may be any of a variety of different translocation types,including, for example, translocations between different chromosomes,whether to the same or different regions, between different regions ofthe same chromosome.

Again, as with the example illustrated in FIG. 1, above, conventionalsequencing starts by breaking up the sequences 202 and 204 in Panel Iinto small fragments and producing short sequence reads 208 from thosefragments, as shown in Panel IL. Because these sequence fragments 208are relatively short, the context of the translocated sequence 206,i.e., as originating from a variant location on the same or a differentsequence, is easily lost during the assembly process. Further, becauseof their short read lengths, sequence assemblies are often predicated onthe use of a reference sequence that would, almost by definition, notreflect structural variations. As such, the short sequence reads 208would invariably be assembled to disregard the proper location of thetranslocated sequence 206, and would instead assemble the non-variantsequences 210 and 212, as shown in Panel IIIa.

In contrast, using the methods and systems described herein, the shortsequence reads derived from sequences 202 and 204, are provided with acompartmentalization, shown in Panel IIb as groups 214 and 216, thatretain the original molecular grouping of the smaller sequencefragments, allowing their assembly as sequences 218 and 220, shown inPanel IIIb, allowing attribution back to the originating sequences 202and 204, and identification of the translocation variation, e.g.,translocated sequence segment 206 a in correct sequence assemblies 218and 220, as illustrated in Panel Mb.

As noted above, the methods and systems described herein provideindividual molecular context for short sequence reads of longer nucleicacids. As used herein, individual molecular context refers to sequencecontext beyond the specific sequence read, e.g., relation to adjacent orproximal sequences, that are not included within the sequence readitself, and as such, will generally be such that they would not beincluded in whole or in part in a short sequence read, e.g., a read ofabout 150 bases, or about 300 bases for paired reads. In some aspects,the methods and systems provide long range sequence context for shortsequence reads. Such long range context includes relationship or linkageof a given sequence read to sequence reads that are within a distance ofeach other of longer than 1 kilobase (kb), longer than 5 kb, longer than10 kb, longer than 15 kb, longer than 20 kb, longer than 30 kb, longerthan 40 kb, longer than 50 kb, longer than 60 kb, longer than 70 kb,longer than 80 kb, longer than 90 kb or even longer than 100 kb, orlonger. By providing longer range individual molecular context, themethods and systems described herein also provide much longer inferredmolecular context. Sequence context, as described herein can includelower resolution context, e.g., from mapping the short sequence reads tothe individual longer molecules or contigs of linked molecules, as wellas the higher resolution sequence context, e.g., from long rangesequencing of large portions of the longer individual molecules, e.g.,having contiguous determined sequences of individual molecules wheresuch determined sequences are longer than 1 kb, longer than 5 kb, longerthan 10 kb, longer than 15 kb, longer than 20 kb, longer than 30 kb,longer than 40 kb, longer than 50 kb, longer than 60 kb, longer than 70kb, longer than 80 kb, longer than 90 kb or even longer than 100 kb. Aswith sequence context, the attribution of short sequences to longernucleic acids, e.g., both individual long nucleic acid molecules orcollections of linked nucleic acid molecules or contigs, may includeboth mapping of short sequences against longer nucleic acid stretches toprovide high level sequence context, as well as providing assembledsequences from the short sequences through these longer nucleic acids.

Furthermore, while one may utilize the long range sequence contextassociated with long individual molecules, having such long rangesequence context also allows one to infer even longer range sequencecontext. By way of one example, by providing the long range molecularcontext described above, one can identify overlapping variant portions,e.g., phased variants, translocated sequences, etc., among longsequences from different originating molecules, allowing the inferredlinkage between those molecules. Such inferred linkages or molecularcontexts are referred to herein as “inferred contigs”. In some caseswhen discussed in the context of phased sequences, the inferred contigsmay represent commonly phased sequences, e.g., where by virtue ofoverlapping phased variants, one can infer a phased contig ofsubstantially greater length than the individual originating molecules.These phased contigs are referred to herein as “phase blocks”.

By starting with longer single molecule reads, one can derive longerinferred contigs or phase blocks than would otherwise be attainableusing short read sequencing technologies or other approaches to phasedsequencing. See, e.g., published U.S. Patent Publication No.2013/0157870, the full disclosure of which is herein incorporated byreference in its entirety. In particular, using the methods and systemsdescribed herein, one can obtain inferred contig or phase block lengthshaving an N50 (the contig or phase block length for which the collectionof all phase blocks or contigs of that length or longer contain at leasthalf of the sum of the lengths of all contigs or phase blocks, and forwhich the collection of all contigs or phase blocks of that length orshorter also contains at least half the sum of the lengths of allcontigs or phase blocks), mode, mean, or median of at least about 10kilobases (kb), at least about 20 kb, at least about 50 kb. In someaspects, inferred contig or phase block lengths have an N50, mode, mean,or median of at least about 100 kb, at least about 150 kb, at leastabout 200 kb, and in some cases, at least about 250 kb, at least about300 kb, at least about 350 kb, at least about 400 kb, and in some cases,at least about 500 kb, at least about 750 kb, at least about 1 Mb, atleast about 1.75 Mb, at least about 2.5 Mb or more, are attained. Instill other cases, maximum inferred contig or phase block lengths of atleast or in excess of 20 kb, 40 kb, 50 kb, 100 kb, 200 kb, 300 kb, 400kb, 500 kb, 750 kb, 1 megabase (Mb), 1.75 Mb, 2 Mb or 2.5 Mb may beobtained. In still other cases, inferred contigs or phase blocks lengthscan be at least about 20 kb, at least about 40 kb, at least about 50 kb,at least about 100 kb, at least about 200 kb, and in some cases, atleast about 500 kb, at least about 750 kb, at least about 1 Mb, and insome cases at least about 1.75 Mb, at least about 2.5 Mb or more.

In one aspect, the methods and systems described herein provide for thecompartmentalization, depositing or partitioning of sample nucleicacids, or fragments thereof, into discrete compartments or partitions(referred to interchangeably herein as partitions), where each partitionmaintains separation of its own contents from the contents of otherpartitions. Unique identifiers, e.g., barcodes, may be previously,subsequently or concurrently delivered to the partitions that hold thecompartmentalized or partitioned sample nucleic acids, in order to allowfor the later attribution of the characteristics, e.g., nucleic acidsequence information, to the sample nucleic acids included within aparticular compartment, and particularly to relatively long stretches ofcontiguous sample nucleic acids that may be originally deposited intothe partitions.

The sample nucleic acids can be partitioned such that the nucleic acidsare present in the partitions in relatively long fragments or stretchesof contiguous nucleic acid molecules. These fragments can represent anumber of overlapping fragments of the overall sample nucleic acids tobe analyzed, e.g., an entire chromosome, exome, or other large genomicfragment. These sample nucleic acids may include whole genomes,individual chromosomes, exomes, amplicons, or any of a variety ofdifferent nucleic acids of interest. In some cases, these fragments ofthe sample nucleic acids may be longer than 100 bases, longer 500 bases,longer than 1 kb, longer than 5 kb, longer than 10 kb, longer than 15kb, longer than 20 kb, longer than 30 kb, longer than 40 kb, longer than50 kb, longer than 60 kb, longer than 70 kb, longer than 80 kb, longerthan 90 kb or even longer than 100 kb, which permits the longer rangemolecular context described above.

The sample nucleic acids can also be partitioned at a level whereby agiven partition has a very low probability of including two overlappingfragments of the starting sample nucleic acid. This can be accomplishedby providing the sample nucleic acid at a low input amount and/orconcentration during the partitioning process. As a result, in somecases, a given partition may include a number of long, butnon-overlapping fragments of the starting sample nucleic acids. Thesample nucleic acids in the different partitions are then associatedwith unique identifiers, where for any given partition, nucleic acidscontained therein possess the same unique identifier, but wheredifferent partitions may include different unique identifiers. Moreover,because the partitioning allocates the sample components into very smallvolume partitions or droplets, it will be appreciated that in order toachieve the allocation as set forth above, one need not conductsubstantial dilution of the sample, as would can be required in highervolume processes, e.g., in tubes, or wells of a multiwell plate.Further, because the systems described herein employ such high levels ofbarcode diversity, one can allocate diverse barcodes among highernumbers of genomic equivalents, as provided above. In particular,previously described, multiwell plate approaches (see, e.g., U.S. PatentPublication No. 2013/0079231 and 2013/0157870, the full disclosures ofwhich are herein incorporated by reference in their entireties) may onlyoperate with a hundred to a few hundred different barcode sequences, andemploy a limiting dilution process of their sample in order to be ableto attribute barcodes to different cells/nucleic acids. As such, theygenerally operate with far fewer than 100 cells, which would can providea ratio of genomes:(barcode type) on the order of 1:10, and certainlywell above 1:100. The systems described herein, on the other hand,because of the high level of barcode diversity, e.g., in excess of10,000, 100,000, 500,000, etc. diverse barcode types, can operate atgenome:(barcode type) ratios that are on the order of 1:50 or less,1:100 or less, 1:1000 or less, or even smaller ratios, while alsoallowing for loading higher numbers of genomes (e.g., on the order ofgreater than 100 genomes per assay, greater than 500 genomes per assay,1000 genomes per assay, or even more) while still providing for farimproved barcode diversity per genome.

Often, the sample is combined with a set of oligonucleotide tags thatare releasably-attached to beads prior to the partitioning. Theoligonucleotides may comprise at least a first and second region. Thefirst region may be a barcode region that, as between oligonucleotideswithin a given partition, may be substantially the same barcodesequence, but as between different partitions, may and, in most cases isa different barcode sequence. The second region may be a an N-mer (e.g.,either a random N-mer or an N-mer designed to target a particularsequence) that can be used to prime the nucleic acids within the samplewithin the partitions. In some cases, where the N-mer is designed totarget a particular sequence, it may be designed to target a particularchromosome (e.g., chromosome 1, 13, 18, or 21), or region of achromosome, e.g., an exome or other targeted region. In some cases, theN-mer may be designed to target a particular gene or genetic region,such as a gene or region associated with a disease or disorder (e.g.,cancer). Within the partitions, an amplification reaction may beconducted using the second N-mer to prime the nucleic acid sample atdifferent places along the length of the nucleic acid. As a result ofthe amplification, each partition may contain amplified products of thenucleic acid that are attached to an identical or near-identicalbarcode, and that may represent overlapping, smaller fragments of thenucleic acids in each partition. The bar-code can serve as a marker thatsignifies that a set of nucleic acids originated from the samepartition, and thus potentially also originated from the same strand ofnucleic acid. Following amplification, the nucleic acids may be pooled,sequenced, and aligned using a sequencing algorithm. Because shortersequence reads may, by virtue of their associated barcode sequences, bealigned and attributed to a single, long fragment of the sample nucleicacid, all of the identified variants on that sequence can be attributedto a single originating fragment and single originating chromosome.Further, by aligning multiple co-located variants across multiple longfragments, one can further characterize that chromosomal contribution.Accordingly, conclusions regarding the phasing of particular geneticvariants may then be drawn. Such information may be useful foridentifying haplotypes, which are generally a specified set of geneticvariants that reside on the same nucleic acid strand or on differentnucleic acid strands. Copy number variations may also be identified inthis manner.

The described methods and systems provide significant advantages overcurrent nucleic acid sequencing technologies and their associated samplepreparation methods. Haplotype phasing and copy number variation dataare generally not available by sequencing genomic DNA because biologicalsamples (blood, cells, or tissue samples, for example) are processed enmasse to extract the genetic material from an ensemble of cells, andconvert it into sequencing libraries that are configured specificallyfor a given sequencing technology. As a result of this ensemble sampleprocessing approach, sequencing data generally provides non-phasedgenotypes, in which it is not possible to determine whether geneticinformation is present on the same or different chromosomes.

In addition to the inability to attribute genetic characteristics to aparticular chromosome, such ensemble sample preparation and sequencingmethods are also predisposed towards primarily identifying andcharacterizing the majority constituents in the sample, and are notdesigned to identify and characterize minority constituents, e.g.,genetic material contributed by one chromosome, or by one or a fewcells, or fragmented tumor cell DNA molecule circulating in thebloodstream, that constitute a small percentage of the total DNA in theextracted sample. The described methods and systems also provide asignificant advantage for detecting minor populations that are presentin a larger sample. As such, they can be useful for assessing copynumber variations in a sample since often only a small portion of aclinical sample contains tissue with copy number variations. Forexample, if the sample is a blood sample from a pregnant woman, only asmall fraction of the sample would contain circulating cell-free fetalDNA.

The use of the barcoding technique disclosed herein confers the uniquecapability of providing individual molecular context for a given set ofgenetic markers, i.e., attributing a given set of genetic markers (asopposed to a single marker) to individual sample nucleic acid molecules,and through variant coordinated assembly, to provide a broader or evenlonger range inferred individual molecular context, among multiplesample nucleic acid molecules, and/or to a specific chromosome. Thesegenetic markers may include specific genetic loci, e.g., variants, suchas SNPs, or they may include short sequences. Furthermore, the use ofbarcoding confers the additional advantages of facilitating the abilityto discriminate between minority constituents and majority constituentsof the total nucleic acid population extracted from the sample, e.g. fordetection and characterization of circulating tumor DNA in thebloodstream, and also reduces or eliminates amplification bias duringany amplification. In addition, implementation in a microfluidics formatconfers the ability to work with extremely small sample volumes and lowinput quantities of DNA, as well as the ability to rapidly process largenumbers of sample partitions (e.g., droplets) to facilitate genome-widetagging.

As described previously, an advantage of the methods and systemsdescribed herein is that they can achieve results through the use ofubiquitously available, short read sequencing technologies. Suchtechnologies have the advantages of being readily available and widelydispersed within the research community, with protocols and reagentsystems that are well characterized and highly effective. These shortread sequencing technologies include those available from, e.g.,Illumina, Inc. (e.g., GXII, NextSeq, MiSeq, HiSeq, X10), Ion Torrentdivision of Thermo-Fisher (e.g., Ion Proton and Ion PGM), pyrosequencingmethods, as well as others.

Of particular advantage is that the methods and systems described hereinutilize these short read sequencing technologies and do so with theirassociated low error rates. In particular, the methods and systemsdescribed herein achieve individual molecular read lengths or context,as described above, but with individual sequencing reads, excluding matepair extensions, that are shorter than 1000 bp, shorter than 500 bp,shorter than 300 bp, shorter than 200 bp, shorter than 150 bp or evenshorter; and with sequencing error rates for such individual molecularread lengths that are less than 5%, less than 1%, less than 0.5%, lessthan 0.1%, less than 0.05%, less than 0.01%, less than 0.005%, or evenless than 0.001%.

II. Work Flow Overview

In one exemplary aspect, the methods and systems described in thedisclosure provide for depositing or partitioning individual samples(e.g., nucleic acids) into discrete partitions, where each partitionmaintains separation of its own contents from the contents in otherpartitions. As used herein, the partitions refer to containers orvessels that may include a variety of different forms, e.g., wells,tubes, micro or nanowells, through holes, or the like. In some aspects,however, the partitions are flowable within fluid streams. These vesselsmay be comprised of, e.g., microcapsules or micro-vesicles that have anouter barrier surrounding an inner fluid center or core, or they may bea porous matrix that is capable of entraining and/or retaining materialswithin its matrix. In some aspects, however, these partitions maycomprise droplets of aqueous fluid within a non-aqueous continuousphase, e.g., an oil phase. A variety of different vessels are describedin, for example, U.S. patent application Ser. No. 13/966,150, filed Aug.13, 2013. Likewise, emulsion systems for creating stable droplets innon-aqueous or oil continuous phases are described in detail in, e.g.,U.S. Patent Publication No. 2010/0105112, the full disclosure of whichis herein incorporated by reference in its entirety. In certain cases,microfluidic channel networks can be suited for generating partitions asdescribed herein. Examples of such microfluidic devices include thosedescribed in detail in U.S. Provisional Patent Application No.61/977,804, filed Apr. 10, 2014, the full disclosure of which isincorporated herein by reference in its entirety for all purposes.Alternative mechanisms may also be employed in the partitioning ofindividual cells, including porous membranes through which aqueousmixtures of cells are extruded into non-aqueous fluids. Such systems aregenerally available from, e.g., Nanomi, Inc.

In the case of droplets in an emulsion, partitioning of samplematerials, e.g., nucleic acids, into discrete partitions may generallybe accomplished by flowing an aqueous, sample containing stream, into ajunction into which is also flowing a non-aqueous stream of partitioningfluid, e.g., a fluorinated oil, such that aqueous droplets are createdwithin the flowing stream partitioning fluid, where such dropletsinclude the sample materials. As described below, the partitions, e.g.,droplets, can also include co-partitioned barcode oligonucleotides. Therelative amount of sample materials within any particular partition maybe adjusted by controlling a variety of different parameters of thesystem, including, for example, the concentration of sample in theaqueous stream, the flow rate of the aqueous stream and/or thenon-aqueous stream, and the like. The partitions described herein areoften characterized by having extremely small volumes. For example, inthe case of droplet based partitions, the droplets may have overallvolumes that are less than 1000 picoliters (pL), less than 900 pL, lessthan 800 pL, less than 700 pL, less than 600 pL, less than 500 pL, lessthan 400 pL, less than 300 pL, less than 200 pL, less than 100 pL, lessthan 50 pL, less than 20 pL, less than 10 pL, or even less than 1 pL.Where co-partitioned with beads, it will be appreciated that the samplefluid volume within the partitions may be less than 90% of the abovedescribed volumes, less than 80%, less than 70%, less than 60%, lessthan 50%, less than 40%, less than 30%, less than 20%, or even less than10% the above described volumes. In some cases, the use of low reactionvolume partitions can be advantageous in performing reactions with verysmall amounts of starting reagents, e.g., input nucleic acids. Methodsand systems for analyzing samples with low input nucleic acids arepresented in U.S. Provisional Patent Application No. 62/017,580, filedJun. 26, 2014, the full disclosure of which is hereby incorporated byreference in its entirety.

Once the samples are introduced into their respective partitions, inaccordance with the methods and systems described herein, the samplenucleic acids within partitions are generally provided with uniqueidentifiers such that, upon characterization of those nucleic acids theymay be attributed as having been derived from their respective origins.Accordingly, the sample nucleic acids can be co-partitioned with theunique identifiers (e.g., barcode sequences). In some aspects, theunique identifiers are provided in the form of oligonucleotides thatcomprise nucleic acid barcode sequences that may be attached to thosesamples. The oligonucleotides are partitioned such that as betweenoligonucleotides in a given partition, the nucleic acid barcodesequences contained therein are the same, but as between differentpartitions, the oligonucleotides can have differing barcode sequences.In some aspects, only one nucleic acid barcode sequence may beassociated with a given partition, although in some cases, two or moredifferent barcode sequences may be present.

The nucleic acid barcode sequences can include from 6 to about 20 ormore nucleotides within the sequence of the oligonucleotides. Thesenucleotides may be completely contiguous, i.e., in a single stretch ofadjacent nucleotides, or they may be separated into two or more separatesubsequences that are separated by one or more nucleotides. In somecases, separated subsequences may be from about 4 to about 16nucleotides in length.

The co-partitioned oligonucleotides can also comprise other functionalsequences useful in the processing of the partitioned nucleic acids.These sequences include, e.g., targeted or random/universalamplification primer sequences for amplifying the genomic DNA from theindividual nucleic acids within the partitions while attaching theassociated barcode sequences, sequencing primers, hybridization orprobing sequences, e.g., for identification of presence of thesequences, or for pulling down barcoded nucleic acids, or any of anumber of other potential functional sequences. Again, co-partitioningof oligonucleotides and associated barcodes and other functionalsequences, along with sample materials is described in, for example,U.S. Provisional Patent Application Nos. 61/940,318, filed Feb. 7, 2014,61/991,018, Filed May 9, 2014, and U.S. patent application Ser. No.14/316,383, filed on Jun. 26, 2014, as well as U.S. patent applicationSer. No. 14/175,935, filed Feb. 7, 2014, the full disclosures of whichis hereby incorporated by reference in their entireties.

Briefly, in one exemplary process, beads are provided that each mayinclude large numbers of the above described oligonucleotides releasablyattached to the beads, where all of the oligonucleotides attached to aparticular bead may include the same nucleic acid barcode sequence, butwhere a large number of diverse barcode sequences may be representedacross the population of beads used. In some cases, the population ofbeads may provide a diverse barcode sequence library that may include atleast 1000 different barcode sequences, at least 10,000 differentbarcode sequences, at least 100,000 different barcode sequences, or insome cases, at least 1,000,000 different barcode sequences.Additionally, each bead may be provided with large numbers ofoligonucleotide molecules attached. In particular, the number ofmolecules of oligonucleotides including the barcode sequence on anindividual bead may be at least bout 10,000 oligonucleotides, at least100,000 oligonucleotide molecules, at least 1,000,000 oligonucleotidemolecules, at least 100,000,000 oligonucleotide molecules, and in somecases at least 1 billion oligonucleotide molecules.

The oligonucleotides may be releasable from the beads upon theapplication of a particular stimulus to the beads. In some cases, thestimulus may be a photo-stimulus, e.g., through cleavage of aphoto-labile linkage that may release the oligonucleotides. In somecases, a thermal stimulus may be used, where elevation of thetemperature of the beads environment may result in cleavage of a linkageor other release of the oligonucleotides form the beads. In some cases,a chemical stimulus may be used that cleaves a linkage of theoligonucleotides to the beads, or otherwise may result in release of theoligonucleotides from the beads.

In accordance with the methods and systems described herein, the beadsincluding the attached oligonucleotides may be co-partitioned with theindividual samples, such that a single bead and a single sample arecontained within an individual partition. In some cases, where singlebead partitions are desired, the relative flow rates of the fluids canbe controlled such that, on average, the partitions contain less thanone bead per partition, in order to ensure that those partitions thatare occupied, are primarily singly occupied. Likewise, one may wish tocontrol the flow rate to provide that a higher percentage of partitionsare occupied, e.g., allowing for only a small percentage of unoccupiedpartitions. In some aspects, the flows and channel architectures arecontrolled as to ensure a desired number of singly occupied partitions,less than a certain level of unoccupied partitions and less than acertain level of multiply occupied partitions.

FIG. 3 illustrates an example method for barcoding and subsequentlysequencing a sample nucleic acid, such as for use for a copy numbervariation or haplotype assay. First, a sample comprising nucleic acidmay be obtained from a source, 300, and a set of barcoded beads may alsobe obtained, 310. The beads can be linked to oligonucleotides containingone or more barcode sequences, as well as a primer, such as a randomN-mer or other primer. In some cases, the barcode sequences arereleasable from the barcoded beads, e.g., through cleavage of a linkagebetween the barcode and the bead or through degradation of theunderlying bead to release the barcode, or a combination of the two. Forexample, in some aspects, the barcoded beads can be degraded ordissolved by an agent, such as a reducing agent to release the barcodesequences. In this example, a low quantity of the sample comprisingnucleic acid, 305, barcoded beads, 315, and, in some cases, otherreagents, e.g., a reducing agent, 320, are combined and subject topartitioning. By way of example, such partitioning may involveintroducing the components to a droplet generation system, such as amicrofluidic device, 325. With the aid of the microfluidic device 325, awater-in-oil emulsion 330 may be formed, where the emulsion containsaqueous droplets that contain sample nucleic acid, 305, reducing agent,320, and barcoded beads, 315. The reducing agent may dissolve or degradethe barcoded beads, thereby releasing the oligonucleotides with thebarcodes and random N-mers from the beads within the droplets, 335. Therandom N-mers may then prime different regions of the sample nucleicacid, resulting in amplified copies of the sample after amplification,where each copy is tagged with a barcode sequence, 340. In some cases,each droplet contains a set of oligonucleotides that contain identicalbarcode sequences and different random N-mer sequences. Subsequently,the emulsion is broken, 345 and additional sequences (e.g., sequencesthat aid in particular sequencing methods, additional barcodes, etc.)may be added, via, for example, amplification methods, 350 (e.g., PCR).Sequencing may then be performed, 355, and an algorithm applied tointerpret the sequencing data, 360. Sequencing algorithms are generallycapable, for example, of performing analysis of barcodes to alignsequencing reads and/or identify the sample from which a particularsequence read belongs.

As noted above, while single bead occupancy may be desired, it will beappreciated that multiply occupied partitions, or unoccupied partitionsmay often be present. An example of a microfluidic channel structure forco-partitioning samples and beads comprising barcode oligonucleotides isschematically illustrated in FIG. 4. As shown, channel segments 402,404, 406, 408 and 410 are provided in fluid communication at channeljunction 412. An aqueous stream comprising the individual samples 414 isflowed through channel segment 402 toward channel junction 412. Asdescribed elsewhere herein, these samples may be suspended within anaqueous fluid prior to the partitioning process.

Concurrently, an aqueous stream comprising the barcode carrying beads416 is flowed through channel segment 404 toward channel junction 412. Anon-aqueous partitioning fluid is introduced into channel junction 412from each of side channels 406 and 408, and the combined streams areflowed into outlet channel 410. Within channel junction 412, the twocombined aqueous streams from channel segments 402 and 404 are combined,and partitioned into droplets 418, that include co-partitioned samples414 and beads 416. As noted previously, by controlling the flowcharacteristics of each of the fluids combining at channel junction 412,as well as controlling the geometry of the channel junction, one canoptimize the combination and partitioning to achieve a desired occupancylevel of beads, samples or both, within the partitions 418 that aregenerated.

As will be appreciated, a number of other reagents may be co-partitionedalong with the samples and beads, including, for example, chemicalstimuli, nucleic acid extension, transcription, and/or amplificationreagents such as polymerases, reverse transcriptases, nucleosidetriphosphates or NTP analogues, primer sequences and additionalcofactors such as divalent metal ions used in such reactions, ligationreaction reagents, such as ligase enzymes and ligation sequences, dyes,labels, or other tagging reagents.

Once co-partitioned, the oligonucleotides disposed upon the bead may beused to barcode and amplify the partitioned samples. An example processfor use of these barcode oligonucleotides in amplifying and barcodingsamples is described in detail in U.S. Patent Application Nos.61/940,318, filed Feb. 7, 2014, 61/991,018, Filed May 9, 2014, and U.S.patent application Ser. No. 14/316,383, filed on Jun. 26, 2014, the fulldisclosures of which are hereby incorporated by reference in theirentireties. Briefly, in one aspect, the oligonucleotides present on thebeads that are co-partitioned with the samples and released from theirbeads into the partition with the samples. The oligonucleotides caninclude, along with the barcode sequence, a primer sequence at its5′end. This primer sequence may be a random oligonucleotide sequenceintended to randomly prime numerous different regions of the samples, orit may be a specific primer sequence targeted to prime upstream of aspecific targeted region of the sample.

Once released, the primer portion of the oligonucleotide can anneal to acomplementary region of the sample. Extension reaction reagents, e.g.,DNA polymerase, nucleoside triphosphates, co-factors (e.g., Mg²⁺ or Mn²⁺etc.), that are also co-partitioned with the samples and beads, thenextend the primer sequence using the sample as a template, to produce acomplementary fragment to the strand of the template to which the primerannealed, with complementary fragment includes the oligonucleotide andits associated barcode sequence. Annealing and extension of multipleprimers to different portions of the sample may result in a large poolof overlapping complementary fragments of the sample, each possessingits own barcode sequence indicative of the partition in which it wascreated. In some cases, these complementary fragments may themselves beused as a template primed by the oligonucleotides present in thepartition to produce a complement of the complement that again, includesthe barcode sequence. In some cases, this replication process isconfigured such that when the first complement is duplicated, itproduces two complementary sequences at or near its termini, to allowthe formation of a hairpin structure or partial hairpin structure, thatreduces the ability of the molecule to be the basis for producingfurther iterative copies. A schematic illustration of one example ofthis is shown in FIG. 5.

As the figure shows, oligonucleotides that include a barcode sequenceare co-partitioned in, e.g., a droplet 502 in an emulsion, along with asample nucleic acid 504. As noted elsewhere herein, the oligonucleotides508 may be provided on a bead 506 that is co-partitioned with the samplenucleic acid 504, which oligonucleotides can be releasable from the bead506, as shown in panel A. The oligonucleotides 508 include a barcodesequence 512, in addition to one or more functional sequences, e.g.,sequences 510, 514 and 516. For example, oligonucleotide 508 is shown ascomprising barcode sequence 512, as well as sequence 510 that mayfunction as an attachment or immobilization sequence for a givensequencing system, e.g., a P5 sequence used for attachment in flow cellsof an Illumina Hiseq or Miseq system. As shown, the oligonucleotidesalso include a primer sequence 516, which may include a random ortargeted N-mer for priming replication of portions of the sample nucleicacid 504. Also included within oligonucleotide 508 is a sequence 514which may provide a sequencing priming region, such as a “read1” or R1priming region, that is used to prime polymerase mediated, templatedirected sequencing by synthesis reactions in sequencing systems. Insome cases, the barcode sequence 512, immobilization sequence 510 and R1sequence 514 may be common to all of the oligonucleotides attached to agiven bead. The primer sequence 516 may vary for random N-mer primers,or may be common to the oligonucleotides on a given bead for certaintargeted applications.

Based upon the presence of primer sequence 516, the oligonucleotides areable to prime the sample nucleic acid as shown in panel B, which allowsfor extension of the oligonucleotides 508 and 508 a using polymeraseenzymes and other extension reagents also co-portioned with the bead 506and sample nucleic acid 504. As shown in panel C, following extension ofthe oligonucleotides that, for random N-mer primers, would anneal tomultiple different regions of the sample nucleic acid 504; multipleoverlapping complements or fragments of the nucleic acid are created,e.g., fragments 518 and 520. Although including sequence portions thatare complementary to portions of sample nucleic acid, e.g., sequences522 and 524, these constructs are generally referred to herein ascomprising fragments of the sample nucleic acid 504, having the attachedbarcode sequences. As will be appreciated, the replicated portions ofthe template sequences as described above are often referred to hereinas “fragments” of that template sequence. Notwithstanding the foregoing,however, the term “fragment” encompasses any representation of a portionof the originating nucleic acid sequence, e.g., a template or samplenucleic acid, including those created by other mechanisms of providingportions of the template sequence, such as actual fragmentation of agiven molecule of sequence, e.g., through enzymatic, chemical ormechanical fragmentation. In some aspects, however, fragments of atemplate or sample nucleic acid sequence may denote replicated portionsof the underlying sequence or complements thereof.

The barcoded nucleic acid fragments may then be subjected tocharacterization, e.g., through sequence analysis, or they may befurther amplified in the process, as shown in panel D. For example,additional oligonucleotides, e.g., oligonucleotide 508 b, also releasedfrom bead 306, may prime the fragments 518 and 520. In particular,again, based upon the presence of the random N-mer primer 516 b inoligonucleotide 508 b (which in some cases can be different from otherrandom N-mers in a given partition, e.g., primer sequence 516), theoligonucleotide anneals with the fragment 518, and is extended to createa complement 526 to at least a portion of fragment 518 which includessequence 528, that comprises a duplicate of a portion of the samplenucleic acid sequence. Extension of the oligonucleotide 508 b continuesuntil it has replicated through the oligonucleotide portion 508 offragment 518. As noted elsewhere herein, and as illustrated in panel D,the oligonucleotides may be configured to prompt a stop in thereplication by the polymerase at a desired point, e.g., afterreplicating through sequences 516 and 514 of oligonucleotide 508 that isincluded within fragment 518. As described herein, this may beaccomplished by different methods, including, for example, theincorporation of different nucleotides and/or nucleotide analogues thatare not capable of being processed by the polymerase enzyme used. Forexample, this may include the inclusion of uracil containing nucleotideswithin the sequence region 512 to prevent a non-uracil tolerantpolymerase to cease replication of that region. As a result a fragment526 is created that includes the full-length oligonucleotide 508 b atone end, including the barcode sequence 512, the attachment sequence510, the R1 primer region 514, and the random N-mer sequence 516 b. Atthe other end of the sequence can be included the complement 516′ to therandom N-mer of the first oligonucleotide 508, as well as a complementto all or a portion of the R1 sequence, shown as sequence 514′. The R1sequence 514 and its complement 514′ are then able to hybridize togetherto form a partial hairpin structure 528. As will be appreciated becausethe random N-mers differ among different oligonucleotides, thesesequences and their complements would not be expected to participate inhairpin formation, e.g., sequence 516′, which is the complement torandom N-mer 516, would not be expected to be complementary to randomN-mer sequence 516 b. This would not be the case for other applications,e.g., targeted primers, where the N-mers would be common amongoligonucleotides within a given partition.

By forming these partial hairpin structures, it allows for the removalof first level duplicates of the sample sequence from furtherreplication, e.g., preventing iterative copying of copies. The partialhairpin structure also provides a useful structure for subsequentprocessing of the created fragments, e.g., fragment 526.

All of the fragments from multiple different partitions may then bepooled for sequencing on high throughput sequencers as described herein.Because each fragment is coded as to its partition of origin, thesequence of that fragment may be attributed back to its origin basedupon the presence of the barcode. This is schematically illustrated inFIG. 6. As shown in one example, a nucleic acid 604 originated from afirst source 600 (e.g., individual chromosome, strand of nucleic acid,etc.) and a nucleic acid 606 derived from a different chromosome 602 orstrand of nucleic acid are each partitioned along with their own sets ofbarcode oligonucleotides as described above.

Within each partition, each nucleic acid 604 and 606 is then processedto separately provide overlapping set of second fragments of the firstfragment(s), e.g., second fragment sets 608 and 610. This processingalso provides the second fragments with a barcode sequence that is thesame for each of the second fragments derived from a particular firstfragment. As shown, the barcode sequence for second fragment set 608 isdenoted by “1” while the barcode sequence for fragment set 610 isdenoted by “2”. A diverse library of barcodes may be used todifferentially barcode large numbers of different fragment sets.However, it is not necessary for every second fragment set from adifferent first fragment to be barcoded with different barcodesequences. In some cases, multiple different first fragments may beprocessed concurrently to include the same barcode sequence. Diversebarcode libraries are described in detail elsewhere herein.

The barcoded fragments, e.g., from fragment sets 608 and 610, may thenbe pooled for sequencing using, for example, sequence by synthesistechnologies available from Illumina or Ion Torrent division of ThermoFisher, Inc. Once sequenced, the sequence reads 612 can be attributed totheir respective fragment set, e.g., as shown in aggregated reads 614and 616, at least in part based upon the included barcodes, and in somecases, in part based upon the sequence of the fragment itself. Theattributed sequence reads for each fragment set are then assembled toprovide the assembled sequence for each sample fragment, e.g., sequences618 and 620, which in turn, may be further attributed back to theirrespective original chromosomes (600 and 602). Methods and systems forassembling genomic sequences are described in, for example, U.S.Provisional Patent Application No. 62/017,589, filed Jun. 26, 2014, thefull disclosure of which is hereby incorporated by reference in itsentirety. In some examples, genomic sequences are assembled by de novoassembly and/or reference based assembly (e.g., mapping to a reference).

III. Application of Methods and Systems to Phasing and Copy NumberAssays

In one aspect of the systems and methods described herein, the abilityto attribute sequence reads to longer originating molecules is used indetermining phase information about the sequence. In one example,barcodes associated with sequences that reveal two or more specific genevariant sequences (e.g., alleles, genetic markers) are compared todetermine whether or not that set of genetic markers reside on the samechromosome or different chromosomes in the sample. Such phasinginformation can be used in order to determine the relative copy numberof certain target chromosomes or genes in a sample. An advantage of thedescribed methods and symptoms is that multiple locations, loci,variants, etc. can be used to identify individual chromosomes or nucleicacid strands from which they originate in order to determine phasing andcopy number information. Often, multiple locations (e.g., greater than2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100, 500, 1000, 5000, 10000,50000, 100000, or 500000) along a chromosome are used in order todetermine phasing, haplotype and copy number variation informationdescribed herein.

By way of example, as noted above, the methods and systems describedherein, by virtue of the partitioning and attribution aspects describedabove, can be useful at providing effective long sequence reads fromindividual nucleic acid fragments, e.g., individual nucleic acidmolecules, despite utilizing sequencing technology that may providerelatively shorter sequence reads. Because these long sequence reads maybe attributed to single starting fragments or molecules, variantlocations in the sequence can, likewise, be attributed to a singlemolecule, and by extrapolation, to a single chromosome. In addition, onemay employ the multiple locations on any given fragment, as alignmentfeatures for adjacent fragments, to provide aligned sequences that canbe inferred as originating from the same chromosome. By way of example,a first fragment may be sequenced, and by virtue of the attributionmethods and systems described above, the variants present on thatsequence may all be attributed to a single chromosome. A second fragmentthat shares a plurality of these variants that are determined to bepresent only on one chromosome, may then be assumed to be derived fromthe same chromosome, and thus aligned with the first, to create a phasedalignment of the two fragments. Repeating this allows for theidentification of long range phase information. Identification ofvariants on a single chromosome can be obtained from either knownreferences, e.g., HapMap, or from an aggregation of the sequencing data,e.g., showing differing variants on an otherwise identical sequencestretch.

FIG. 7 provides a schematic illustration of an example phased sequencingprocess. As shown, an originating nucleic acid 702, such as, forexample, a chromosome, a chromosome fragment, an exome, or other large,single nucleic acid molecule, can be fragmented into multiple largefragments 704, 706, 708. The originating nucleic acid 702 may include anumber of sequence variants (A, B, C, D, E, F, and G) that are specificto the particular nucleic acid molecule, e.g., chromosome. In accordancewith the processes described herein, the originating nucleic acid can befragmented into multiple large, overlapping fragments 704, 706 and 708,that include subsets of the associated sequence variants. Each fragmentcan then be partitioned, further fragmented into subfragments, andbarcoded, as described herein to provide multiple overlapping, barcodedsubfragments of the larger fragments, where subfragments of a givenlarger fragment bear the same barcode sequence. For example,subfragments associated with barcode sequence “1” and barcode sequence“2” are shown in partitions 710 and 712, respectively, The barcodedsubfragments can then be pooled, sequenced, and the sequencedsubfragments assembled to provide long fragment sequences 714, 716, and717. One or more of the long fragment sequences 714, 716, and 717 caninclude multiple variants. The long fragment sequences may then befurther assembled, based upon overlapping phased variant informationfrom sequences 714, 716, and 717 to provide a phased sequence 718, fromwhich phased locations can be determined.

Once the phased locations are determined, one may further exploit thatinformation in a variety of ways. For example, one can utilize knowledgeof phased variants in assessing genetic risk for certain disorders,identify paternal vs. maternal characteristics, identify aneuploidies,or identify haplotyping information.

In some aspects of the systems and methods disclosed herein, copy numbervariation assays are performed using simultaneous detection of two ormore phased genetic markers to improve the accuracy of copy numbercounting. Utilizing the phasing information can increase the relativestrength of the signal compared to the variance under a naïve methodjust based on counting reads over multiple loci and across haplotypes.Additionally, utilizing phasing information allows for normalization ofposition-specific biases, boosting the signal substantially further.Copy number variation (CNV) accuracy may depend on myriad factorsincluding sequencing depth, length of CNV, number of copies, etc). Themethods and systems provided herein may determine CNV with an accuracyof at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 99%, 99.1%,99.2%, 99.3% 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, 99.95%, 99.99%,99.995%, or 99.999%. In some cases, the methods and systems providedherein determine CNV with an error rate of less than 10%, 9%, 8%, 7%,6%, 5%, 4%, 3%, 2%, 1%, 0.1%, 0.05%, 0.01%, 0.005%, 0.001%, 0.0005%,0.0001%, 0.00005%, 0.00001%, or 0.000005%. Similarly, the methods andsystems provided herein may detect phasing/haplotype information of twoor more genetic variants with an accuracy of at least 70%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 99%, 99.1%, 99.2%, 99.3% 99.4%, 99.5%,99.6%, 99.7%, 99.8%, 99.9%, 99.95%, 99.99%, 99.995%, or 99.999%. In somecases, the methods and systems provided herein determine phasing orhaplotype information with an error rate of less than 10%, 9%, 8%, 7%,6%, 5%, 4%, 3%, 2%, 1%, 0.1%, 0.05%, 0.01%, 0.005%, 0.001%, 0.0005%,0.0001%, 0.00005%, 0.00001%, or 0.000005%. This disclosure also providesmethods of removing locus-specific biases, where the locus-specificvariance are reduced by at least 2-fold, 3-fold, 4-fold, 5-fold,10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 70-fold, 80-fold,90-fold, 100-fold, 200-fold, 500-fold, 1000-fold, 5000-fold, or10000-fold. The methods and systems provided herein can be used todetect variations in copy number, such as where the change in copynumber reflects a change in the number of chromosomes, or portions ofchromosomes. In some cases, the methods and systems provided herein canbe used to detect variations in copy number of a gene present on thesame chromosome.

FIG. 8 (top panel) is a schematic illustrating a subset of a healthypatient's genome. This patient has a heterozygous genotype at theindicated loci and two separate haplotypes (1 and 2) 805, 810 located onseparate chromosome strands. The patient's naturally-occurringvariations (such as SNPs or indels) are depicted as circles. FIG. 8 alsodepicts the genome of a patient with cancer 815. Certain cancers areassociated with a gain in haplotype copy number. The middle paneldepicts a gain in a haplotype 2, 810. Cancers may also be associatedwith a loss in haplotype number, as depicted in the bottom panel of FIG.8, which shows a loss of haplotype 2 820. Common sequencing techniquescannot accurately determine this loss or gain of haplotype copies. Asshown in FIG. 9a this is in part due to the fact that thetumor-contributed DNA 910 in a patient's blood is only a small fractionof the total DNA, of which a majority is the DNA contributed by normaltissue 905. This low concentration of tumor DNA results in imprecisedetection of copy number with normal sequencing techniques, see FIG. 9b. The difference in the peaks of expected counts at mean depth D 935 forno copy variation 920 and the peaks for copy loss 925 (940) and copygain 930 (945) is difficult to detect. For any given individual marker,the distribution of results of the copy number assay in replicatetesting can be distributed around the correct answer in a mannerapproximating a Poisson distribution, where the width of thedistribution is dependent on various sources of random error in theassay. Since for a give sample the change in copy number may berelatively small portion of the sample, broad probability distributionsfor monitoring of single genetic markers can mask the correct result.This difficulty is due to the fact that normal sequencing techniquesonly look at one single variant position of a haplotype at a time, asshown in FIG. 10 (left panel). Using such techniques, there can besignificant overlap between peaks representing copy loss 1025, normalcopy 1020, and copy gain 1030. The techniques disclosed herein allow fordetection of whole (or partial) haplotypes, increasing the resolutionand improving the detection of copy gain and loss, FIG. 10 (rightpanel). This improvement is schematically shown in FIG. 11, where normaldetection 1100 results in spread out, overlapping peaks while thetechniques herein 1110 allow for finer peaks and improved resolution ofcopy gain or loss. The use of simultaneous monitoring of two or morephased genetic markers, particularly markers that are known to beco-located on a single chromosome, and which can therefore most likelyalways appear in greater or lesser number in a synchronized, non-randomfashion has the effect of narrowing the width of the expected resultsdistribution and simultaneously improving the accuracy of the count.

In addition to advantages in detecting and diagnosing cancers, themethods and systems provided herein also provide more accurate andsensitive processes for detecting fetal aneuploidy.

Fetal aneuploidies are aberrations in fetal chromosome number.Aneuploidies commonly result in significant physical and neurologicalimpairments. For example, a reduction in the number of X chromosomes isresponsible for Turner's syndrome. An increase in copy number ofchromosome number 21 results in Down Syndrome. Invasive testing such asamniocentesis or Chorionic Villus Sampling (CVS) can lead to risk ofpregnancy loss and less invasive methods of testing the maternal bloodare used here.

Methods described herein may be useful in non-invasively detecting fetalaneuploidies. An exemplary process is shown in FIG. 12. A pregnant womanat risk of carrying a fetus with an aneuploid genome is tested, 1200. Amaternal blood sample containing fetal genetic material is collected,1205. Genetic material (e.g., cell-free nucleic acids) is then extractedfrom the blood sample, 1210. A set of barcoded beads may also beobtained, 1215. The beads can be linked to oligonucleotides containingone or more barcode sequences, as well as a primer, such as a randomN-mer or other primer. In some cases, the barcode sequences arereleasable from the barcoded beads, e.g., through cleavage of a linkagebetween the barcode and the bead or through degradation of theunderlying bead to release the barcode, or a combination of the two. Forexample, in some aspects, the barcoded beads can be degraded ordissolved by an agent, such as a reducing agent to release the barcodesequences. In this example, a sample, 1210, barcoded beads, 1220, and,in some cases, other reagents, e.g., a reducing agent, are combined andsubjected to partitioning. By way of example, such partitioning mayinvolve introducing the components to a droplet generation system, suchas a microfluidic device, 1225. With the aid of the microfluidic device1225, a water-in-oil emulsion 1230 may be formed, where the emulsioncontains aqueous droplets that contain sample nucleic acid, 1210,barcoded beads, 1215, and, in some cases, a reducing agent. The reducingagent may dissolve or degrade the barcoded beads, thereby releasing theoligonucleotides with the barcodes and random N-mers from the beadswithin the droplets, 1235. The random N-mers may then prime differentregions of the sample nucleic acid, resulting in amplified copies of thesample after amplification, where each copy is tagged with a barcodesequence, 1240. In some cases, each droplet contains a set ofoligonucleotides that contain identical barcode sequences and differentrandom N-mer sequences. In other embodiments, individual dropletscomprise unique bar-code sequences; or, in some cases, a certainproportion of the total population of droplets has unique sequences.Subsequently, the emulsion is broken, 1245 and additional sequences(e.g., sequences that aid in particular sequencing methods, additionalbarcodes, etc.) may be added, via, for example, amplification methods(e.g., PCR). Sequencing may then be performed via any suitable type ofsequencing platform (e.g., Illumina, Ion Torrent, Pacific BiosciencesSMRT, Roche 454 sequencing SOLiD sequencing, etc.), 1250, and analgorithm applied to interpret the sequencing data, 1255. Sequencingalgorithms are generally capable, for example, of performing analysis ofbarcodes to align sequencing reads and/or identify the sample from whicha particular sequence read belongs. The aligned sequences may be furtherattributed to their respective genetic origins (e.g., chromosomes) basedupon, the unique barcodes attached. The number of chromosome copies isthen compared to that of a normal diploid chromosome, 1260. The patientis informed of any copy number aberrations for different chromosomes andthe associated risks/disease, 1265.

Phasing, e.g. determining whether genetic variants are linked or resideon different chromosomes can provide useful information for a variety ofapplications. By way of example, phasing is useful for determining ifcertain translocations of a genome associated with diseases are present.Detection of such translocations can also allow for differentialdiagnosis and modified treatment. Determination of which alleles in agenome are linked can be useful for considering how genes are inherited.

It can often be useful to know the pattern of alleles, the haplotype,for each individual chromosome of a chromosome pair. For example, twocopies of an inactivating mutation present on one chromosome may be oflimited consequence, but could have significant effect if distributedbetween the two chromosomes, e.g., where neither chromosome suppliesactive gene product. These effects can be expressed e.g., with increasedrisk of disease or lack of response to certain medications.

IV. Application of Methods and Systems toIdentification/Characterization of Structural Variations

In other applications, the method and systems described herein arehighly useful in obtaining the long range molecular sequence informationfor identification and characterization of a wide range of differentgenetic structural variations. As noted above, these variations includea wide variety of different variant events, including insertions,deletions, duplications, retrotransposons, translocations, inversionsshort and long tandem repeats, and the like. These structural variationsare of significant scientific interest, as they are believed to beassociated with a range of diverse genetic diseases.

Despite the interest in these variations, there are few effective andefficient methods of identifying and characterizing these structuralvariations. In part, this is because these variations are notcharacterized by the presence of abnormal sequence segments, butinstead, involve and abnormal sequence context of what would beconsidered normal sequence segments, or simply missing sequenceinformation. Because of their relatively short read lengths, mostsequencing technologies are unable to provide significant context, andespecially, long range sequence context, e.g., beyond their readlengths, for the sequence reads they produce, and thus lose theidentification of these variations in the assembly process. Thedifficulties in identifying these variations is further complicated bythe ensemble approach of these technologies in which many molecules,e.g., multiple chromosomes, are combined to yield a consensus sequencethat may include genomic material that both includes and does notinclude the variation.

In the context of the presently described methods and systems, however,one can utilize short read sequencing technologies to derive long rangesequence information that is attributable to individual originatingnucleic acid molecules, and thus retain the long range sequence contextof variant regions contained in whole or in part in those individualmolecules.

As described above, the methods and systems described herein are capableof providing long range sequence information that is attributable toindividual originating nucleic acid molecules, and further, inpossessing this long range sequence information, inferring even longerrange sequence context, through the comparing and overlapping of theselonger sequence information. Such long range sequence information and/orinferred sequence context allows the identification and characterizationnumerous structural variations not easily identified using availabletechniques.

While illustrated in simplified fashion in FIG. 2, FIGS. 13A and 13Bprovide a more detailed example process for identifying certain types ofstructural variations using the methods and systems described herein. Asshown, the genome of an organism, or tissue from an organism, mightordinarily include the first genotype illustrated in FIG. 13A, where afirst gene region 1302 including first gene 1304 is separated from asecond gene region 1306 including second gene 1208. This separation mayreflect a range of distances between the genes, including, e.g.,different regions in the same exon, different exons on the samechromosome, different chromosomes, etc. As shown in FIG. 13B however, agenotype is shown that reflects a translocation event having occurred inwhich gene 1308 is inserted into gene region 1304 such that it creates agene fusion between genes 1304 and 1308 as gene fusion 1312 in variantsequence 1314.

Current methods for detecting large genomic structural variants (such aslarge inversions or translocations) rely on read pairs that span thebreakpoints of the variants (for example the genomic loci where thetranslocated parts fused together). To ensure that such read pairs areobserved during a sequencing experiment, very deep sequencing can berequired. In targeted sequencing (such as exome sequencing), detectingstructural variants with current sequencing technologies is almostimpossible, unless the breakpoint is within the targeted regions (e.g.in an exon), which is very unlikely.

Information provided by the barcode methods and systems describedherein, however, can greatly improve the ability to detect structuralvariants. Intuitively, the loci to the left and to the right of abreakpoint, can tend to be on a common fragment of genomic DNA andtherefore be maintained within a single partition, and thus barcodedwith a common or shared barcode sequence. Due to the stochastic natureof shearing, this sharing of barcodes decreases as the sequences aremore distant from the breakpoint. Using statistical methods one candetermine whether the barcode overlap between two genomic loci issignificantly larger than what would be expected by chance. Such anoverlap suggests the presence of a breakpoint. Importantly, the barcodeinformation complements information provided by traditional sequencing(such as information from reads spanning the breakpoint) if suchinformation is available.

In the context of the methods described herein, the genomic materialfrom the organism, including the relevant gene regions is fragmentedsuch that it includes relatively long fragments, as described above.This is illustrated with respect to the non-translocated genotype inFIG. 13A. As shown two long individual first molecule fragments 1316 and1318 are created that include gene regions 1302 and 1306 respectively.These fragments are separately partitioned into partitions 1320 and1322, respectively, and each of the first fragments is fragmented into anumber of second fragments 1324 and 1326, respectively within thepartition, which fragmenting process attaches a unique identifier tag orbarcode sequence to the second fragments that is common to all of thesecond fragments within a given partition. The tag or barcode isindicated by “1” or “2”, for each of partitions 1320 and 1322,respectively. As a result, completely separate genes 1304 and 1308 canresult in differently partitioned, and differently barcoded groups ofsecond fragments.

Once barcoded, the second fragments may then be pooled and subjected tonucleic acid sequencing processes, which can provide both the sequenceof the second fragment as well as the barcode sequence for thatfragment. Based upon the presence of a particular barcode, e.g., 1 or 2,a the second fragment sequences may then be attributed to a certainoriginating sequence, e.g., gene 1304 or 1308, as shown by theattribution of barcodes to each sequence. In some cases, mapping ofbarcoded second fragment sequences as to separate originating firstfragment sequences may be sufficiently definitive to determine that notranslocation has occurred. However, in some cases, one may assemble thesecond fragment sequences to provide an assembled sequence for all or aportion of the originating first fragment sequence, e.g., as shown byassembled sequences 1330 and 1332.

In contrast to the non-translocated genotype example shown in FIG. 13A,FIG. 13B shows a schematic illustration of the same process applied to atranslocation containing genotype. As shown, a first long nucleic acidfragment 1352 is generated from the variant sequence 1314, and includesat least a portion of the translocation variant, e.g., gene fusion 1312.The first fragment 1352 is then partitioned into discrete partition1354. Within partition 1354, first fragment 1352 is further fragmentedinto second fragments 1356 that again, include unique barcodes that arethe same for all second fragments 1356 within the partition 1354 (shownas barcode “1”). As above, pooling the second fragments and sequencingprovides the underlying sequences of the second fragments as well astheir associated barcodes. These barcoded sequences can then beattributed to their respective gene sequences. As shown, however, bothgenes can reflect attributed second fragment sequences that include thesame barcode sequences, indicating that they originated from the samepartition, and potentially the same originating molecule, indicating agene fusion. This may be further validated by providing a number ofoverlapping first fragments that also include at least portions of thegene fusion, but processed in different partitions with differentbarcodes.

In some cases, the presence of multiple different barcode sequences (andtheir underlying fragment sequences) that attribute to each of theoriginally separated genes can be indicative of the presence of a genefusion or other translocation event. In some cases, attribution of atleast 2 barcodes, at least 3 different barcodes, at least 4 differentbarcodes, at least 5 different barcodes, at least 10 different barcodes,at least 20 different barcodes or more, to two genetic regions thatwould have been expected to have been separated based upon a referencesequence, may provide indication of a translocation event that hasplaced those regions proximal to, adjacent to or otherwise integratedwith each other. In some cases, the size of the fragments that arepartitioned can indicate the sensitivity with which one can identifyvariant linkage. In particular, where the fragments in a given dropletare 10 kb in length, it would be expected that linkages that are withinthat 10 kb size range would be detectable.

Likewise, where both the variant and the wild type structure fall withinthe same 10 kb fragment, it would be expected that identification ofthat variant would be more difficult, as both would show linkage throughcommon or shared barcodes. As such, fragment size selection may be usedto adjust the relative proximity of detected linked sequences, whetheras wild type or variants. In general, however, structural variants thatresult in proximal sequences that are normally separated by more than100 bases, more than 500 bases, more than 1 kb, 10 kb, more than 20 kb,more than 30 kb, more than 40 kb, more than 50 kb, more than 60 kb, morethan 70 kb, more than 80 kb, more than 90 kb, more than 100 kb, morethan 200 kb or even greater, may be readily identified herein byidentifying the linkage between those unlinked sequence segments invariant genomes, which linkage is indicated by shared or commonbarcodes, and/or, as noted, by sequence data that spans a breakpoint.Such linkage is generally identifiable when those linked sequences areseparated within the genomic sequence by less than 50 kb, less than 40kb, less than 30 kb, less than 20 kb, less than 10 kb, less than 5 kb,less than 4 kb, less than 3 kb, less than 2 kb, less than 1 kb, lessthan 500 bases, less than 200 bases or even less.

In some cases, a structural variation resulting in two sequences beingpositioned proximal to each other or linked, where they would normallybe separated by, e.g., more than 10 kb, more than 20 kb, more than 30kb, more than 40 kb, or more than 50 kb or more, may be identified bythe percentage of the total number of mappable barcoded sequences thatinclude barcodes that are common to the two sequence portions.

As will be appreciated, in some cases, the processes described hereincan ensure that sequences that are within a certain sequence distancewill be included, whether as wild type or variant sequences, within asingle partition, e.g., as a single nucleic acid fragment. For example,where common or overlapping barcode sequences are greater than 1% of thetotal number of barcodes mapped to the two sequences, it may be used toidentify linkage as between two sequence segments, and particularly, asbetween two sequence segments that would not normally be linked, e.g., astructural variation. In some cases, the shared or common barcodes canbe more than 2%, more than 3%, more than 4%, more than 5%, more than 6%,more than 7%, more than 8%, and in some cases more than 9% or even morethan 10% of the total mappable barcodes to two normally separatedsequences, in order to identify a structural linkage that constitutes astructural variation within the genome. In some cases, the shared orcommon barcodes can be detected at a proportion or number that isstatistically significantly greater than a control genome that is knownnot to have the structural variation. Additionally, where secondsequence fragments span the point where the variant sequence meets the“normal” sequence, or “breakpoint”, e.g., as in second fragment 1358 onecan use this information as additional evidence of the gene fusion.

Again, as above, one can further elucidate the structure of the genefusion 1312, by assembling the second fragment sequences to yield theassembled sequence of the gene fusion 1312, shown as assembled sequence1360.

Further, while the presence of the barcode sequences allows the assemblyof the short sequences into sequences for the longer originatingfragments, these longer fragments also permit the inference of longerrange sequence information from overlapping long fragments assembledfrom different, overlapping originating long fragments. This resultingassembly allows for longer range sequence level identification andcharacterization of gene fusion 1312.

In some cases, the methods described above are useful in identifying thepresence of retrotransposons. Retrotransposons can be created bytranscription followed by reverse transcription of spliced messenger RNA(mRNA) and insertion into a new location in the genome. Hence, thesestructural variants lack introns and are often interchromosomal butotherwise have diverse features. When retrotransposons introducefunctional copies of genes they are referred to as retrogenes, whichhave been reported in human and Drosophila genomes. In other cases,retrocopies may contain the entire transcript, specific transcriptisoforms or an incomplete transcript. In addition, alternativetranscription start sites and promoter sequences sometimes reside withina transcript so retrotransposons sometimes introduce promotor sequenceswithin the reinserted region of the genome that could drive expressionof downstream sequences.

Unlike tandem duplications, retrotransposons insert far away from theparental gene within exons or introns. When inserted near genesretrotransposons can exploit local regulatory sequences for expression.Insertions near genes can also inactivate the receiving gene or createnew chimera transcripts. Retrotransposon mediated chimeric genetranscripts have been reported in RNA-Seq data from human samples.

Despite the significance of retrotransposons their detection can belimited to directed approaches relying on paired read support from matepair libraries, exon-exon junction discovery in whole genome sequencing(WGS) or RNA-Seq recognition of retrotransposon chimeras. All of thesemethods can have false positives that complicate analysis.

Retrotransposons can be identified from whole genome libraries using thesystems and methods described herein, and their insertion site can bemapped using the barcode mapping discussed above. For example, the CephNA12878 genome has a SKA3-DDX10 chimeric retrotransposon. The SKA3intron-less transcript is inserted in between exons 10 and 11 of DDX10.Furthermore the CBX3-C15ORF17 retrotransposon can also be detected inNA12878 using the methods described herein. Isoform 2 of CBX3 isinserted in between exons 2 and 3 of C15ORF17. This chimeric transcripthas been observed in 20% of European RNA-Seq samples from the HapMapproject (D.R. Schrider et al. PLoS Genetics 2013).

Retrotransposons can also be detected in whole exome libraries preparedusing the methods and systems described herein. While retrotransposonsare easily enriched with exome targeting it can be difficult or notpossible to differentiate between a translocation event and aretrotransposon since introns are removed during capture. However, usingthe systems and methods described herein, one may identifyretrotransposons in whole exome sequencing (WES) libraries byintroducing intronic baits for suspected retrotransposons (see also U.S.Provisional Patent Application No. 62/072,164, filed Oct. 29, 2014,incorporated herein by reference in its entirety for all purposes). Lackof intron signal can be indicative of retrotransposon structuralvariants whereas intron signal can be indicative of a translocation.

As will be appreciated, the ability to use longer range sequence contextin identifying and characterizing of the above-described variations isequally applicable to identifying the range of other structuralvariations, including insertions, deletion, retrotransposons,inversions, etc., by mapping barcodes to regions within the variation,and/or spanning the variation.

V. Diseases & Disorders Arising from Copy Number Variation

The present methods and systems provide a highly accurate and sensitiveapproach to diagnosing and/or detecting a wide range of diseases anddisorders. Diseases associated with copy number variations can include,for example, DiGeorge/velocardiofacial syndrome (22q11.2 deletion),Prader-Willi syndrome (15q11-q13 deletion), Williams-Beuren syndrome(7q11.23 deletion), Miller-Dieker syndrome (MDLS) (17p13.3microdeletion), Smith-Magenis syndrome (SMS) (17p11.2 microdeletion),Neurofibromatosis Type 1 (NF1) (17q11.2 microdeletion), Phelan-McErmidSyndrome (22q13 deletion), Rett syndrome (loss-of-function mutations inMECp2 on chromosome Xq28), Merzbacher disease (CNV of PLP1), spinalmuscular atrophy (SMA) (homozygous absence of telomerec SMN1 onchromosome 5q13), Potocki-Lupski Syndrome (PTLS, duplication ofchromosome 17p.11.2). Additional copies of the PMP22 gene can beassociated with Charcot-Marie-Tooth neuropathy type IA (CMT1A) andhereditary neuropathy with liability to pressure palsies (HNPP). Thedisease can be a disease described in Lupski J. (2007) Nature Genetics39: S43-S47.

The methods and systems provided herein can also accurately detect ordiagnose a wide range of fetal aneuploidies. Often, the methods providedherein comprise analyzing a sample (e.g., blood sample) taken from apregnant woman in order to evaluate the fetal nucleic acids within thesample. Fetal aneuploidies, can include, e.g., trisomy 13 (Patausyndrome), trisomy 18 (Edwards syndrome), trisomy 21 (Down Syndrome),Klinefelter Syndrome (XXY), monosomy of one or more chromosomes (Xchromosome monosomy, Turner's syndrome), trisomy X, trisomy of one ormore chromosomes, tetrasomy or pentasomy of one or more chromosomes(e.g., XXXX, XXYY, XXXY, XYYY, XXXXX, XXXXY, XXXYY, XYYYY and XXYYY),triploidy (three of every chromosome, e.g. 69 chromosomes in humans),tetraploidy (four of every chromosome, e.g. 92 chromosomes in humans),and multiploidy. In some embodiments, an aneuploidy can be a segmentalaneuploidy. Segmental aneuploidies can include, e.g., 1p36 duplication,dup(17)(p11.2p11.2) syndrome, Down syndrome, Pelizaeus-Merzbacherdisease, dup(22)(q11.2q11.2) syndrome, and cat-eye syndrome. In somecases, an abnormal genotype, e.g., fetal genotype, is due to one or moredeletions of sex or autosomal chromosomes, which can result in acondition such as Cri-du-chat syndrome, Wolf-Hirschhorn, Williams-Beurensyndrome, Charcot-Marie-Tooth disease, Hereditary neuropathy withliability to pressure palsies, Smith-Magenis syndrome,Neurofibromatosis, Alagille syndrome, Velocardiofacial syndrome,DiGeorge syndrome, Steroid sulfatase deficiency, Kallmann syndrome,Microphthalmia with linear skin defects, Adrenal hypoplasia, Glycerolkinase deficiency, Pelizaeus-Merzbacher disease, Testis-determiningfactor on Y, Azospermia (factor a), Azospermia (factor b), Azospermia(factor c), or 1p36 deletion. In some embodiments, a decrease inchromosomal number results in an XO syndrome

Excessive genomic DNA copy number variation is also associated withLi-Fraumeni cancer predisposition syndrome (Shlien et al. (2008) PNAS105:11264-9). CNV is associated with malformation syndromes, includingCHARGE (coloboma, heart anomaly, choanal atresia, retardation, genital,and ear anomalies), Peters-Plus, Pitt-Hopkins, andthrombocytopenia-absent radius syndrome (see e.g., Ropers HH (2007) Am Jof Hum Genetics 81: 199-207). The relationship between copy numbervariations and cancer is described, e.g., in Shlien A. and Malkin D.(2009) Genome Med. 1(6): 62. Copy number variations are associated with,e.g., autism, schizophrenia, and idiopathic learning disability. Seee.g., Sebat J., et al. (2007) Science 316: 445-9; Pinto J. et al.

As described herein, the methods and systems provided herein are alsouseful to detect CNVs associated with different types of cancer. Forexample, the methods and systems can be used to detect EGFR copy number,which can be increased in non-small cell lung cancer.

The methods and systems provided herein can also be used to determine asubject's level of susceptibility to a particular disease or disorder,including susceptibility to infection from a pathogen (e.g., viral,bacterial, microbial, fungal, etc.). For example, the methods can beused to determine a subject's susceptibility to HIV infection byanalyzing the copy number of CCL3L1, given that a relatively high levelof CCL3L1 is associated with lower susceptibility to HIV infection(Gonzalez E. et al. (2005) Science 307: 1434-1440). In another example,the methods can be used to determine a subject's susceptibility tosystem lupus erythematosus. In such cases, for example, the methods canbe used to detect copy number of FCGR3B (CD16 cell surfaceimmunoglobulin receptor) since a low copy number of this molecule isassociated with an increased susceptibility to systemic lupuserythematosus (Aitman T. J. et al. (2006) Nature 439: 851-855). Themethods and systems provided herein can also be used to detect CNVsassociated with other diseases or disorders, such as CNVs associatedwith autism, schizophrenia, or idiopathic learning disability (Kinght etal., (1999) The Lancet 354 (9191): 1676-81.). Similarly, the methods andsystems can be used to detect autosomal-dominant microtia, which islinked to five tandem copies of a copy-number-variable region atchromosome 4p16 (Balikova I. (2008) Am J. Hum Genet. 82: 181-187).

VI. Detection, Diagnosis and Treatment of Diseases and Disorders

The methods and systems provided herein can also assist with thedetection, diagnosis, and treatment of a disease or disorder. In somecases, a method comprises detecting a disease or disorder using a systemor method described herein and further providing a treatment to asubject based on the detection of the disease. For example, if a canceris detected, the subject may be treated by a surgical intervention, byadministering a drug designed to treat such cancer, by providing ahormonal therapy, and/or by administering radiation or more generalizedchemotherapy.

Often, the methods and systems also permit a differential diagnosis andmay further comprise treating a patient with a targeted therapy. Ingeneral, differential diagnosis of a disease or disorder (or absencethereof) can be achieved by determining and characterizing a sequence ofa sample nucleic acid obtained from a subject suspected of having thedisease or disorder and further characterizing the sample nucleic acidas indicative of a disorder or disease state (or absence thereof) bycomparing it to a sequence and/or sequence characterization of areference nucleic acid indicative of the presence (or absence) of thedisorder or disease state.

The reference nucleic acid sequence may be derived from a genome that isindicative of an absence of a disease or disorder state (e.g., germlinenucleic acid) or may be derived from a genome that is indicative of adisease or disorder state (e.g., cancer nucleic acid, nucleic acidindicative of an aneuploidy, etc.). Moreover, the reference nucleic acidsequence (e.g., having lengths of longer than 1 kb, longer than 5 kb,longer than 10 kb, longer than 15 kb, longer than 20 kb, longer than 30kb, longer than 40 kb, longer than 50 kb, longer than 60 kb, longer than70 kb, longer than 80 kb, longer than 90 kb or even longer than 100 kb)may be characterized in one or more respects, with non-limiting examplesthat include determining the presence (or absence) of a particularsequence, determining the presence (or absence) of a particularhaplotype, determining the presence (or absence) of one or more geneticvariations (e.g., structural variations (e.g., a copy number variation,an insertion, a deletion, a translocation, an inversion, aretrotransposon, a rearrangement, a repeat expansion, a duplication,etc.), single nucleotide polymorphisms (SNPs), etc.) and combinationsthereof. Moreover, any suitable type and number of sequencecharacteristics of the reference sequence can be used to characterizethe sequence of the sample nucleic acid. For example, one or moregenetic variations (or lack thereof) or structural variations (or lackthereof) of a reference nucleic acid sequence may be used as a sequencesignature to identify the reference nucleic acid as indicative of thepresence (or absence) of a disorder or disease state. Based on thecharacterization of the reference nucleic acid sequence utilized, thesample nucleic acid sequence can be characterized in a similar mannerand further characterized/identified as derived (or not derived) from anucleic acid indicative of the disorder or disease based upon whether ornot it displays a similar character to the reference nucleic acidsequence. In some cases, characterizations of sample nucleic acidsequence and/or the reference nucleic acid sequence and theircomparisons may be completed with the aid of a programmed computerprocessor. In some cases, such a programmed computer processor can beincluded in a computer control system, such as in an example computercontrol system described elsewhere herein.

The sample nucleic acid may be obtained from any suitable source,including sample sources and biological sample sources describedelsewhere herein. In some cases, the sample nucleic acid may comprisecell-free nucleic acid. In some cases, the sample nucleic acid maycomprise tumor nucleic acid (e.g., tumor DNA). In some cases, the samplenucleic acid may comprise circulating tumor nucleic acid (e.g.,circulating tumor DNA (ctDNA)). Circulating tumor nucleic acid may bederived from a circulating tumor cell (CTC) and/or may be obtained, forexample, from a subject's blood, plasma, other bodily fluid or tissue.

FIGS. 20-21 illustrate an example method for characterizing a samplenucleic acid in the context of disease detection and diagnosis. FIG. 20demonstrates an example method by which long range sequence context canbe determined for a reference nucleic acid (e.g., germline nucleic acid(e.g., germline genomic DNA), nucleic acid associated with a particulardisorder or disease state) from shorter barcoded fragments, such as, forexample in a manner analogous to that shown in FIG. 6. With respect toFIG. 20, a reference nucleic acid may be obtained 2000, and a set ofbarcoded beads may also be obtained, 2010. The beads can be linked tooligonucleotides containing one or more barcode sequences, as well as aprimer, such as a random N-mer or other primer. In some cases, thebarcode sequences are releasable from the barcoded beads, e.g., throughcleavage of a linkage between the barcode and the bead or throughdegradation of the underlying bead to release the barcode, or acombination of the two. For example, in some aspects, the barcoded beadscan be degraded or dissolved by an agent, such as a reducing agent torelease the barcode sequences. In this example, reference nucleic acid,2005, barcoded beads, 2015, and, in some cases, other reagents, e.g., areducing agent, 2020, are combined and subject to partitioning. In somecases, the reference nucleic acid 2000 may be fragmented prior topartitioning and at least some of the resulting fragments arepartitioned as 2005 for barcoding. By way of example, such partitioningmay involve introducing the components to a droplet generation system,such as a microfluidic device, 2025. With the aid of the microfluidicdevice 2025, a water-in-oil emulsion 2030 may be formed, where theemulsion contains aqueous droplets that contain reference nucleic acid,2005, reducing agent, 2020, and barcoded beads, 2015. The reducing agentmay dissolve or degrade the barcoded beads, thereby releasing theoligonucleotides with the barcodes and random N-mers from the beadswithin the droplets, 2035. The random N-mers may then prime differentregions of the reference nucleic acid, resulting in amplified copies ofthe reference nucleic acid after amplification, where each copy istagged with a barcode sequence, 2040. In some cases, amplification 2040may be achieved by a method analogous to that described elsewhere hereinand schematically depicted in FIG. 5. In some cases, each dropletcontains a set of oligonucleotides that contain identical barcodesequences and different random N-mer sequences. Subsequently, theemulsion is broken, 2045 and additional sequences (e.g., sequences thataid in particular sequencing methods, additional barcodes, etc.) may beadded, via, for example, amplification methods, 2050 (e.g., PCR).Sequencing may then be performed, 2055, and an algorithm applied tointerpret the sequencing data, 2060. In some cases, interpretation ofthe sequencing data 2060 may include providing a sequence for at least aportion of the reference nucleic acid. In some cases, long rangesequence context for the reference nucleic acid is obtained andcharacterized such as, for example, in the case where the referencenucleic acid is derived from a disease state (e.g., determination of oneor more haplotypes as described elsewhere herein, determination of oneor more structural variations (e.g., a copy number variation, aninsertion, a deletion, a translocation, an inversion, a rearrangement, arepeat expansion, a duplication, retrotransposon, a gene fusion, etc.),calling of one or more SNPs, etc.). In some cases, variants can becalled for various reference nucleic acids obtained from a source andinferred contigs generated to provide longer range sequence context,such as is described elsewhere herein with respect to FIG. 7.

FIG. 21 demonstrates an example of characterizing a sample nucleic acidsequence from the reference 2060 characterization obtained as shown inFIG. 20. Long range sequence context can be obtained for the samplenucleic acid from sequencing of shorter barcoded fragments as isdescribed elsewhere herein, such as, for example, via the methodschematically depicted in FIG. 6. As shown in FIG. 21, a nucleic acidsample (e.g., a sample comprising a circulating tumor nucleic acid) canbe obtained from a subject suspected of having a disorder or disease(e.g., cancer) 2100 and a set of barcoded beads may also be obtained,2110. The beads can be linked to oligonucleotides containing one or morebarcode sequences, as well as a primer, such as a random N-mer or otherprimer. In some cases, the barcode sequences are releasable from thebarcoded beads, e.g., through cleavage of a linkage between the barcodeand the bead or through degradation of the underlying bead to releasethe barcode, or a combination of the two. For example, in some aspects,the barcoded beads can be degraded or dissolved by an agent, such as areducing agent to release the barcode sequences. In this example, samplenucleic acid, 2105, barcoded beads, 2115, and, in some cases, otherreagents, e.g., a reducing agent, 2120, are combined and subject topartitioning. In some cases, the fetal sample 2100 is fragmented priorto partitioning and at least some of the resulting fragments arepartitioned as 2105 for barcoding. By way of example, such partitioningmay involve introducing the components to a droplet generation system,such as a microfluidic device, 2125. With the aid of the microfluidicdevice 2125, a water-in-oil emulsion 2130 may be formed, where theemulsion contains aqueous droplets that contain sample nucleic acid,2105, reducing agent, 2120, and barcoded beads, 2115. The reducing agentmay dissolve or degrade the barcoded beads, thereby releasing theoligonucleotides with the barcodes and random N-mers from the beadswithin the droplets, 2135. The random N-mers may then prime differentregions of the sample nucleic acid, resulting in amplified copies of thesample nucleic acid after amplification, where each copy is tagged witha barcode sequence, 2140. In some cases, amplification 2140 may beachieved by a method analogous to that described elsewhere herein andschematically depicted in FIG. 5. In some cases, each droplet contains aset of oligonucleotides that contain identical barcode sequences anddifferent random N-mer sequences. Subsequently, the emulsion is broken,2145 and additional sequences (e.g., sequences that aid in particularsequencing methods, additional barcodes, etc.) may be added, via, forexample, amplification methods, 2150 (e.g., PCR). Sequencing may then beperformed, 2155, and an algorithm applied to interpret the sequencingdata, 2160. In some cases, interpretation of the sequencing data 2160may include providing a sequence of the sample nucleic acid. In somecases, long range sequence context for the nucleic acid sample isobtained. The sample nucleic acid sequence can be characterized 2160(e.g., determination of one or more haplotypes as described elsewhereherein, determination of one or more structural variations (e.g., a copynumber variation, an insertion, a deletion, a translocation, aninversion, a rearrangement, a repeat expansion, a duplication,retrotransposon, a gene fusion, etc.) using the characterization of thereference nucleic acid sequence 2060. Based on the comparison of thesample nucleic acid sequence and its characterization with the sequenceand characterization of the reference nucleic acid, a differentialdiagnosis 2170 regarding the presence (or absence) of the disorder ordisease state can be made.

As can be appreciated, analysis of reference nucleic acids and samplenucleic acids may completed as separate partitioning analyses or may becompleted as part of a single partitioning analysis. For example, sampleand reference nucleic acids may be added to the same device and barcodedsample and reference fragments generated in droplets according to FIGS.20 and 21, where an emulsion comprises the droplets for both types ofnucleic acid. The emulsion can then be broken and the contents of thedroplets pooled, further processed (e.g., bulk addition of additionalsequences via PCR) and sequenced as described elsewhere herein.Individual sequencing reads from the barcoded fragments can beattributed to their respective sample sequence via barcode sequences.Sequences obtained from the sample nucleic acid can be characterizedbased upon the characterization of the reference nucleic acid sequence.

Utilizing methods and systems herein can improve accuracy in determininglong range sequence context of nucleic acids, including the long-rangesequence context of reference and sample nucleic acid sequences asdescribed herein. The methods and systems provided herein may determinelong-range sequence context of reference and/or sample nucleic acidswith accuracy of at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%,99%, 99.1%, 99.2%, 99.3% 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%,99.95%, 99.99%, 99.995%, or 99.999%. In some cases, the methods andsystems provided herein may determine long-range sequence context ofreference and/or sample nucleic acids with an error rate of less than10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.1%, 0.05%, 0.01%, 0.005%,0.001%, 0.0005%, 0.0001%, 0.00005%, 0.00001%, or 0.000005%.

Moreover, methods and systems herein can also improve accuracy incharacterizing a reference nucleic acid sequence and/or sample nucleicacid sequence in one or more aspects (e.g., determination of a sequence,determination of one or more genetic variations, determination ofhaplotypes, etc.). Accordingly, the methods and systems provided hereinmay characterize a reference nucleic acid sequence and/or sample nucleicacid sequence in one or more aspects with an accuracy of at least 70%,80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 99%, 99.1%, 99.2%, 99.3% 99.4%,99.5%, 99.6%, 99.7%, 99.8%, 99.9%, 99.95%, 99.99%, 99.995%, or 99.999%.In some cases, the methods and systems provided herein may characterizea reference nucleic acid sequence and/or sample nucleic acid sequence inone or more aspects with an error rate of less than 10%, 9%, 8%, 7%, 6%,5%, 4%, 3%, 2%, 1%, 0.1%, 0.05%, 0.01%, 0.005%, 0.001%, 0.0005%,0.0001%, 0.00005%, 0.00001%, or 0.000005%.

Moreover, as is discussed above, improved accuracy in determininglong-range sequence context of reference nucleic acids andcharacterization of the same can result in improved accuracy insequencing and characterizing sample nucleic acids and subsequent use indifferential diagnosis of a disorder or disease. Accordingly, a samplenucleic acid sequence (including long-range sequence context) can beprovided from analysis of a reference nucleic acid sequence with anerror rate of less than 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.1%,0.05%, 0.01%, 0.005%, 0.001%, 0.0005%, 0.0001%, 0.00005%, 0.00001%, or0.000005%. In some cases, a sample nucleic acid sequence can be used fordifferential diagnosis of a disorder or disease (or absence thereof) bycomparison with a sequence and/or characterization of a sequence of areference nucleic acid with accuracy of at least 70%, 80%, 85%, 90%,91%, 92%, 93%, 94%, 95%, 99%, 99.1%, 99.2%, 99.3% 99.4%, 99.5%, 99.6%,99.7%, 99.8%, 99.9%, 99.95%, 99.99%, 99.995%, or 99.999%. In some cases,a sample nucleic acid sequence can be used for differential diagnosis ofa disorder or disease (or absence thereof) by comparison with a sequenceand/or characterization of a sequence of a reference nucleic acid withan error rate of less than 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%,0.1%, 0.05%, 0.01%, 0.005%, 0.001%, 0.0005%, 0.0001%, 0.00005%,0.00001%, or 0.000005%.

In an example, the methods and systems may be used to detect copy numbervariation in a patient with lung cancer in order to determine whetherthe lung cancer is Non-Small Cell Lung Cancer, which is associated witha variation in the EGFR gene. After such diagnosis, a patient'streatment regimen may be refined to correlate with the differentialdiagnosis. Targeted therapy or molecularly targeted therapy is one ofthe major modalities of medical treatment (pharmacotherapy) for cancer,others being hormonal therapy and cytotoxic chemotherapy. Targetedtherapy blocks the growth of cancer cells by interfering with specifictargeted molecules needed for carcinogenesis and tumor growth, ratherthan by simply interfering with all rapidly dividing cells (e.g. withtraditional chemotherapy).

FIG. 14 shows an exemplary process for differentially diagnosingNon-Small Cell Lung Cancer. A patient with chromic cough, weight lossand shortness of breath is tested for lung cancer 1400. Blood is drawnfrom the patient 1405 and samples (e.g., circulating tumor cells,cell-free DNA, circulating nucleic acid (e.g., circulating tumor nucleicacid), etc.) are derived from the blood 1410. A set of barcoded beadsmay also be obtained, 1415. The beads can be linked to oligonucleotidescontaining one or more barcode sequences, as well as a primer, such as arandom N-mer or other primer. In some cases, the barcode sequences arereleasable from the barcoded beads, e.g., through cleavage of a linkagebetween the barcode and the bead or through degradation of theunderlying bead to release the barcode, or a combination of the two. Forexample, in some aspects, the barcoded beads can be degraded ordissolved by an agent, such as a reducing agent to release the barcodesequences. In this example, a sample, 1410, barcoded beads, 1420, and,in some cases, other reagents, e.g., a reducing agent, are combined andsubject to partitioning. By way of example, such partitioning mayinvolve introducing the components to a droplet generation system, suchas a microfluidic device, 1425. With the aid of the microfluidic device1425, a water-in-oil emulsion 1430 may be formed, where the emulsioncontains aqueous droplets that contain sample nucleic acid, 1410,barcoded beads, 1415, and, in some cases, a reducing agent. The reducingagent may dissolve or degrade the barcoded beads, thereby releasing theoligonucleotides with the barcodes and random N-mers from the beadswithin the droplets, 1435. The random N-mers may then prime differentregions of the sample nucleic acid, resulting in amplified copies of thesample after amplification, where each copy is tagged with a barcodesequence, 1440. In some cases, each droplet contains a set ofoligonucleotides that contain identical barcode sequences and differentrandom N-mer sequences. Subsequently, the emulsion is broken, 1445 andadditional sequences (e.g., sequences that aid in particular sequencingmethods, additional barcodes, etc.) may be added, via, for example,amplification methods (e.g., PCR). Sequencing may then be performed,1450, and an algorithm applied to interpret the sequencing data, 1455.Sequencing algorithms are generally capable, for example, of performinganalysis of barcodes to align sequencing reads and/or identify thesample from which a particular sequence read belongs.

The analyzed sequence is then compared to a known genome referencesequence to determine the CNV of different genes 1460. If the EGFR copynumber in the DNA is higher than normal, the patient can bedifferentially diagnosed with non-small cell lung cancer (NSCLC) insteadof small-cell lung cancer 1465. The CTC of non-small cell lung canceralso has other copy number variations that may further distinguish itfrom small-cell lung cancer. Depending on the stage of the cancer,surgery, chemotherapy, or radiation therapy is prescribed 1470. In somecases, a patient diagnosed with NSLC is administered a drug targeted forsuch cancer such as an ALK inhibitor (e.g., Crizotinib). In some casesof variations in EGFR, the patient is administered cetuximab,panitumumab, lapatinib, and/or capecitabine. In a different situation,the target may be a different gene, such as ERBB2, and the therapycomprises trastuzumab (Herceptin). (2010) Nature 466: 368-72; Cook E. H.and Scherer S. W. (2008) Nature 455: 919-923.

The main categories of targeted therapy are small molecules, smallmolecule drug conjugates and monoclonal antibodies. Small molecules mayinclude tyrosine-kinase inhibitors such as Imatinib mesylate (Gleevec,also known as STI-571) (which is approved for chronic myelogenousleukemia, gastrointestinal stromal tumor and some other types ofcancer); Gefitinib (Iressa, also known as ZD1839)(which targets theepidermal growth factor receptor (EGFR) tyrosine kinase and is approvedin the U.S. for non small cell lung cancer); Erlotinib (marketed asTarceva); Bortezomib (Velcade) (which is an apoptosis-inducingproteasome inhibitor drug that causes cancer cells to undergo cell deathby interfering with proteins); tamoxifen; JAK inhibitors (e.g.,tofactinib), ALK inhibitors (e.g., crizotinib.); Bcl-2 inhibitors (e.g.obatoclax in clinical trials, ABT-263, and Gossypol); PARP inhibitors(e.g. Iniparib, Olaparib in clinical trials); PI3K inhibitors (e.g.perifosine in a phase III trial). Apatinib (which is a selective VEGFReceptor 2 inhibitor); AN-152, (AEZS-108) doxorubicin linked to[D-Lys(6)]-LHRH; Braf inhibitors (vemurafenib, dabrafenib, LGX818) (usedto treat metastatic melanoma that harbors BRAF V600E mutation); MEKinhibitors (trametinib, MEK162); CDK inhibitors, e.g. PD-0332991, LEE011in clinical trials; Hsp90 inhibitors; and Salinomycin.

Other therapies include Small Molecule Drug Conjugates such asVintafolide, which is a small molecule drug conjugate consisting of asmall molecule targeting the folate receptor. Monoclonal antibodies areanother type of therapy that may be administered as part of a methodprovided herein. Monoclonal drug conjugates may also be administered.Exemplary monoclonal antibodies include: Rituximab (marketed as MabTheraor Rituxan)(which targets CD20 found on B cells and targets non Hodgkinlymphoma); Trastuzumab (Herceptin) (which targets the Her2/neu (alsoknown as ErbB2) receptor expressed in some types of breast cancer);Cetuximab (marketed as Erbitux) and Panitumumab Bevacizumab (marketed asAvastin) (which targets VEGF ligand).

VII. Characterizing Fetal Nucleic Acid From Parental Nucleic Acid

As noted elsewhere herein, the methods and systems described herein mayalso be used to characterize circulating nucleic acids within the bloodor plasma of a subject. Such analyses include the analysis ofcirculating tumor DNA, for use in identification of potential diseasestates in a patient, or circulating fetal DNA within the blood or plasmaof a pregnant female, in order to characterize the fetal DNA in anon-invasive way, e.g., without resorting to direct sampling throughamniocentesis or other invasive procedures.

In some cases, the methods may be used to characterize fetal nucleicacid sequences, e.g. circulating fetal DNA, based, at least in part, onanalysis of parental nucleic acid sequences. For example, long rangesequence context can be determined for both paternal and maternalnucleic acids (e.g., having lengths of longer than 1 kb, longer than 5kb, longer than 10 kb, longer than 15 kb, longer than 20 kb, longer than30 kb, longer than 40 kb, longer than 50 kb, longer than 60 kb, longerthan 70 kb, longer than 80 kb, longer than 90 kb or even longer than 100kb) from shorter barcoded fragments using methods and systems describedherein. Long range sequence context can be used to determine one or morehaplotypes and one or more genetic variations, including singlenucleotide polymorphisms (SNPs), structural variations in (e.g., a copynumber variation, an insertion, a deletion, a translocation, aninversion, a rearrangement, a repeat expansion, a retrotransposon, aduplication, a gene fusion, etc.) in both the paternal and maternalnucleic acid sequences. Moreover, long range sequence context ofpaternal and maternal nucleic acids and any determined SNP, haplotypeand/or structural variation information can be used to characterize asequence of a fetal nucleic acid obtained from the pregnant mother(e.g., circulating fetal nucleic acid, such as, for example, cell-freefetal nucleic acid). In some cases, characterizations of a fetal nucleicacid, via comparison with maternal and paternal sequences andcharacterization, may be completed with the aid of a programmed computerprocessor. In some cases, such a programmed computer processor can beincluded in a computer control system, such as in an example computercontrol system described elsewhere herein.

For example, a sequence and/or long range sequence context of parentaland/or maternal nucleic acids may be used as a reference by which tocharacterize fetal nucleic acid, including a fetal nucleic acidsequence. Indeed, long range sequence context obtained by methods andsystems described herein can provide improved, long range sequencecontext information for paternal and maternal nucleic acids from whichfetal nucleic acid sequences can be characterized. In some cases,characterization of a fetal nucleic acid sequence from parental nucleicacids as references may include determining a sequence for at least aportion of a fetal nucleic acid, and/or calling one or more SNPs of afetal nucleic acid sequence, determining one or more de novo mutationsof a fetal nucleic acid sequence, determining one or more haplotypes ofa fetal nucleic acid sequence, and/or determining and characterizing oneor more structural variations, etc. in a sequence of the fetal nucleicacid.

FIGS. 17-19 illustrate an example method for characterizing fetalnucleic acid from longer range sequence context obtained for paternaland maternal nucleic acid, via sequencing of shorter barcoded fragments.FIG. 17 demonstrates an example method by which longer range sequencecontext can be determined for a paternal nucleic acid sample (e.g.,paternal genomic DNA) from shorter barcoded fragments, such as, forexample, in a manner analogous to that shown in FIG. 6. With respect toFIG. 17, a sample comprising paternal nucleic acid may be obtained fromthe father of a fetus, 1700, and a set of barcoded beads may also beobtained, 1710. The beads can be linked to oligonucleotides containingone or more barcode sequences, as well as a primer, such as a randomN-mer or other primer. In some cases, the barcode sequences arereleasable from the barcoded beads, e.g., through cleavage of a linkagebetween the barcode and the bead or through degradation of theunderlying bead to release the barcode, or a combination of the two. Forexample, in some aspects, the barcoded beads can be degraded ordissolved by an agent, such as a reducing agent to release the barcodesequences. In this example, paternal sample comprising nucleic acid,1705, barcoded beads, 1715, and, in some cases, other reagents, e.g., areducing agent, 1720, are combined and subject to partitioning. In somecases, the paternal sample 1700 is fragmented prior to partitioning andat least some of the resulting fragments are partitioned as 1705 forbarcoding. By way of example, such partitioning may involve introducingthe components to a droplet generation system, such as a microfluidicdevice, 1725. With the aid of the microfluidic device 1725, awater-in-oil emulsion 1730 may be formed, where the emulsion containsaqueous droplets that contain paternal sample nucleic acid, 1705,reducing agent, 1720, and barcoded beads, 1715. The reducing agent maydissolve or degrade the barcoded beads, thereby releasing theoligonucleotides with the barcodes and random N-mers from the beadswithin the droplets, 1735. The random N-mers may then prime differentregions of the paternal sample nucleic acid, resulting in amplifiedcopies of the paternal sample after amplification, where each copy istagged with a barcode sequence, 1740. In some cases, amplification 1740may be achieved by a method analogous to that described elsewhere hereinand schematically depicted in FIG. 5. In some cases, each dropletcontains a set of oligonucleotides that contain identical barcodesequences and different random N-mer sequences. Subsequently, theemulsion is broken, 1745 and additional sequences (e.g., sequences thataid in particular sequencing methods, additional barcodes, etc.) may beadded, via, for example, amplification methods, 1750 (e.g., PCR).Sequencing may then be performed, 1755, and an algorithm applied tointerpret the sequencing data 1760. In some cases, for example,interpretation of sequencing data 1760 may include providing a sequencefor at least a portion of the paternal nucleic acid. In some cases, longrange sequence context for the paternal nucleic acid sample can beobtained and characterized (e.g., determination of one or morehaplotypes as described elsewhere herein, determination of one or morestructural variations (e.g., a copy number variation, an insertion, adeletion, a translocation, an inversion, a rearrangement, a repeatexpansion, a duplication, a retrotransposon, a gene fusion, etc.),calling of one or more SNPs, determination of one or more other geneticvariations, etc.). In some cases, variants can be called for variouspaternal nucleic acids and inferred contigs generated to provide longerrange sequence context, such as is described elsewhere herein withrespect to FIG. 7.

FIG. 18 demonstrates an example method by which long range sequencecontext can be determined for a maternal nucleic acid sample (e.g.,maternal genomic DNA) from shorter barcoded fragments, such as, forexample, in a manner analogous to that shown in FIG. 6. With respect toFIG. 18, a sample comprising maternal nucleic acid may be obtained fromthe pregnant mother of a fetus, 1800, and a set of barcoded beads mayalso be obtained, 1810. The beads can be linked to oligonucleotidescontaining one or more barcode sequences, as well as a primer, such as arandom N-mer or other primer. In some cases, the barcode sequences arereleasable from the barcoded beads, e.g., through cleavage of a linkagebetween the barcode and the bead or through degradation of theunderlying bead to release the barcode, or a combination of the two. Forexample, in some aspects, the barcoded beads can be degraded ordissolved by an agent, such as a reducing agent to release the barcodesequences. In this example, maternal sample comprising nucleic acid,1805, barcoded beads, 1815, and, in some cases, other reagents, e.g., areducing agent, 1820, are combined and subject to partitioning. In somecases, the maternal sample 1800 is fragmented prior to partitioning andat least some of the resulting fragments are partitioned as 1805 forbarcoding. By way of example, such partitioning may involve introducingthe components to a droplet generation system, such as a microfluidicdevice, 1825. With the aid of the microfluidic device 1825, awater-in-oil emulsion 1830 may be formed, where the emulsion containsaqueous droplets that contain maternal sample nucleic acid, 1805,reducing agent, 1820, and barcoded beads, 1815. The reducing agent maydissolve or degrade the barcoded beads, thereby releasing theoligonucleotides with the barcodes and random N-mers from the beadswithin the droplets, 1835. The random N-mers may then prime differentregions of the maternal sample nucleic acid, resulting in amplifiedcopies of the maternal sample after amplification, where each copy istagged with a barcode sequence, 1840. In some cases, amplification 1840may be achieved by a method analogous to that described elsewhere hereinand schematically depicted in FIG. 5. In some cases, each dropletcontains a set of oligonucleotides that contain identical barcodesequences and different random N-mer sequences. Subsequently, theemulsion is broken, 1845 and additional sequences (e.g., sequences thataid in particular sequencing methods, additional barcodes, etc.) may beadded, via, for example, amplification methods, 1850 (e.g., PCR).Sequencing may then be performed, 1855, and an algorithm applied tointerpret the sequencing data, 1860. In some cases, for example,interpretation of sequencing data 1860 may include providing a sequencefor at least a portion of the maternal nucleic acid. In some cases, longrange sequence context for the maternal nucleic acid sample can beobtained and characterized (e.g., determination of one or morehaplotypes as described elsewhere herein, determination of one or morestructural variations (e.g., a copy number variation, an insertion, adeletion, a translocation, an inversion, a rearrangement, a repeatexpansion, a duplication, a retrotransposon, a gene fusion, etc.),calling of one or more SNPs, determination of one or more other geneticvariations, etc. In some cases, variants can be called for variousmaternal nucleic acids obtained from a sample and inferred contigsgenerated to provide longer range sequence context, such as is describedelsewhere herein with respect to FIG. 7.

FIG. 19 demonstrates an example of characterizing a fetal samplesequence from the paternal 1760 and maternal 1860 characterizationsobtained as shown in FIG. 17 and FIG. 18, respectively. As shown in FIG.19, a fetal nucleic acid sample can be obtained from the pregnant mother1900. Long range sequence context can be obtained for the fetal nucleicacid from sequencing of shorter barcoded fragments as is describedelsewhere herein, such as, for example, via the method schematicallydepicted in FIG. 6. In some cases, the fetal nucleic acid sample may becirculating fetal DNA and/or cell-free DNA that may be, for example,obtained from the pregnant mother's blood, plasma, other bodily fluid,or tissue. A set of barcoded beads may also be obtained, 1910. The beadsare can be linked to oligonucleotides containing one or more barcodesequences, as well as a primer, such as a random N-mer or other primer.In some cases, the barcode sequences are releasable from the barcodedbeads, e.g., through cleavage of a linkage between the barcode and thebead or through degradation of the underlying bead to release thebarcode, or a combination of the two. For example, in some aspects, thebarcoded beads can be degraded or dissolved by an agent, such as areducing agent to release the barcode sequences. In this example, fetalsample comprising nucleic acid, 1905, barcoded beads, 1915, and, in somecases, other reagents, e.g., a reducing agent, 1920, are combined andsubject to partitioning as 1905. In some cases, the fetal sample 1900 isfragmented prior to partitioning and at least some of the resultingfragments are partitioned as 1905 for barcoding. By way of example, suchpartitioning may involve introducing the components to a dropletgeneration system, such as a microfluidic device, 1925. With the aid ofthe microfluidic device 1925, a water-in-oil emulsion 1930 may beformed, where the emulsion contains aqueous droplets that containmaternal sample nucleic acid, 1905, reducing agent, 1920, and barcodedbeads, 1915. The reducing agent may dissolve or degrade the barcodedbeads, thereby releasing the oligonucleotides with the barcodes andrandom N-mers from the beads within the droplets, 1935. The randomN-mers may then prime different regions of the fetal sample nucleicacid, resulting in amplified copies of the fetal sample afteramplification, where each copy is tagged with a barcode sequence, 1940.In some cases, amplification 1940 may be achieved by a method analogousto that described elsewhere herein and schematically depicted in FIG. 5.In some cases, each droplet contains a set of oligonucleotides thatcontain identical barcode sequences and different random N-mersequences. Subsequently, the emulsion is broken, 1945 and additionalsequences (e.g., sequences that aid in particular sequencing methods,additional barcodes, etc.) may be added, via, for example, amplificationmethods, 1950 (e.g., PCR). Sequencing may then be performed, 1955, andan algorithm applied to interpret the sequencing data, 1960. In general,longer range sequence context for the fetal nucleic acid sample can beobtained from the shorter barcoded fragments that are sequenced. In somecases, for example, interpretation of sequencing data 1960 may includeproviding a sequence for at least a portion of the fetal nucleic acid.The fetal nucleic acid sequence can be characterized 1960 (e.g.,determination of one or more haplotypes as described elsewhere herein,determination of one or more structural variations (e.g., a copy numbervariation, an insertion, a deletion, a translocation, an inversion, arearrangement, a repeat expansion, a duplication, retrotransposon, agene fusion, etc.), determination of one or more de novo mutations,calling of one or more SNPs, etc.) using the long-range sequencecontexts and/or characterizations of the paternal 1760 and maternal 1860samples. In some cases, phase blocks of the fetal nucleic acid can bedetermined by comparison of the fetal nucleic acid sequence to thematernal and paternal phase blocks.

As can be appreciated, analysis of paternal nucleic acid, maternalnucleic acid and/or fetal nucleic acid may completed as part of separatepartitioning analyses or may be completed as part of one or morecombined partitioning analyses. For example, paternal, maternal andfetal nucleic acids may be added to the same device and barcodedmaternal, paternal and fetal fragments generated in droplets accordingto FIGS. 17-19, where an emulsion comprises the droplets for the threetypes of nucleic acid. The emulsion can then be broken and the contentsof the droplets pooled, further processed (e.g., bulk addition ofadditional sequences via PCR) and sequenced as described elsewhereherein. Individual sequencing reads from the barcoded fragments can beattributed to their respective sample sequence via barcode sequences.

In some cases, the sequence of a fetal nucleic acid, including thesequence of the fetal genome, and/or genetic variations in the fetalnucleic acid sequence may be determined from long range paternal andmaternal sequence contexts and characterizations obtained using methodsand systems described herein. For example, genome sequencing of paternaland maternal genomes, along with sequencing of circulating fetal nucleicacids, may be used to determine a corresponding fetal genome sequence.An example of determining a sequence of genomic fetal nucleic acid fromsequence analysis of parental genomes and cell-free fetal nucleic acidcan be found in Kitzman et al. (2012 June 6) Sci Transl. Med. 4(137):137ra76, which is herein entirely incorporated by reference.Determination of a fetal genome may be useful in the prenataldetermination and diagnosis of genetic disorders in the fetus,including, for example, fetal aneuploidy. As discussed elsewhere herein,methods and systems provided herein can be useful in resolvinghaplotypes in nucleic acid sequences. Haplotype-resolved paternal andmaternal sequences can be determined for paternal and maternal samplenucleic acid sequences, respectively which can aid in more accuratelydetermining the sequence of a fetal genome and/or characterizing thesame.

Utilizing methods and systems herein can improve accuracy in determininglong range sequence context of nucleic acids, including the long-rangesequence context of parental nucleic acid sequences (e.g., maternalnucleic acid sequences, paternal nucleic acid sequences). The methodsand systems provided herein may determine long-range sequence context ofparental nucleic acids with accuracy of at least 70%, 80%, 85%, 90%,91%, 92%, 93%, 94%, 95%, 99%, 99.1%, 99.2%, 99.3% 99.4%, 99.5%, 99.6%,99.7%, 99.8%, 99.9%, 99.95%, 99.99%, 99.995%, or 99.999%. In some cases,the methods and systems provided herein may determine long-rangesequence context of parental nucleic acids with an error rate of lessthan 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.1%, 0.05%, 0.01%,0.005%, 0.001%, 0.0005%, 0.0001%, 0.00005%, 0.00001%, or 0.000005%.Moreover, methods and systems herein can also improve accuracy incharacterizing a paternal nucleic acid sequence in one or more aspects(e.g., determination of a sequence, determination of one or more geneticvariations, determination of one or more structural variants,determination of haplotypes, etc.). Accordingly, the methods and systemsprovided herein may characterize a paternal nucleic acid sequence in oneor more aspects with an accuracy of at least 70%, 80%, 85%, 90%, 91%,92%, 93%, 94%, 95%, 99%, 99.1%, 99.2%, 99.3% 99.4%, 99.5%, 99.6%, 99.7%,99.8%, 99.9%, 99.95%, 99.99%, 99.995%, or 99.999%. In some cases, themethods and systems provided herein may characterize a parental nucleicacid sequence in one or more aspects with an error rate of less than10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.1%, 0.05%, 0.01%, 0.005%,0.001%, 0.0005%, 0.0001%, 0.00005%, 0.00001%, or 0.000005%.

Moreover, as is discussed above, improved accuracy in determininglong-range sequence context of parental nucleic acids andcharacterization of the same can result in improved accuracy insequencing and characterizing fetal nucleic acids. Accordingly, in somecases, a fetal nucleic acid sequence (including long-range sequencecontext) can be provided from analysis of parental nucleic sequenceswith accuracy of at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%,99%, 99.1%, 99.2%, 99.3% 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%,99.95%, 99.99%, 99.995%, or 99.999%. In some cases, a fetal nucleic acidsequence (including long-range sequence context) can be provided fromanalysis of parental nucleic sequences with an error rate of less than10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.1%, 0.05%, 0.01%, 0.005%,0.001%, 0.0005%, 0.0001%, 0.00005%, 0.00001%, or 0.000005%. In somecases, a fetal nucleic acid sequence can be characterized in one or moreaspects via analysis of parental nucleic acid sequences as describedherein (e.g., determination of a sequence, determination of one or moregenetic variations, determination of one or more structural variations,determination of haplotypes, etc.) with accuracy of at least 70%, 80%,85%, 90%, 91%, 92%, 93%, 94%, 95%, 99%, 99.1%, 99.2%, 99.3% 99.4%,99.5%, 99.6%, 99.7%, 99.8%, 99.9%, 99.95%, 99.99%, 99.995%, or 99.999%.In some cases, a fetal nucleic acid sequence can be characterized in oneor more aspects via analysis of parental nucleic acid sequences asdescribed herein (e.g., determination of a sequence, determination ofone or more genetic variations, determination of haplotypes,determination of one or more structural variations, etc.) with an errorrate of less than 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.1%, 0.05%,0.01%, 0.005%, 0.001%, 0.0005%, 0.0001%, 0.00005%, 0.00001%, or0.000005%.

VIII. Samples

Detection of a disease or disorder may begin with obtaining a samplefrom a patient. The term “sample,” as used herein, generally refers to abiological sample. Examples of biological samples include nucleic acidmolecules, amino acids, polypeptides, proteins, carbohydrates, fats, orviruses. In an example, a biological sample is a nucleic acid sampleincluding one or more nucleic acid molecules. Exemplary samples mayinclude polynucleotides, nucleic acids, oligonucleotides, cell-freenucleic acid (e.g., cell-free DNA (cfDNA)), circulating cell-freenucleic acid, circulating tumor nucleic acid (e.g., circulating tumorDNA (ctDNA)), circulating tumor cell (CTC) nucleic acids, nucleic acidfragments, nucleotides, DNA, RNA, peptide polynucleotides, complementaryDNA (cDNA), double stranded DNA (dsDNA), single stranded DNA (ssDNA),plasmid DNA, cosmid DNA, chromosomal DNA, genomic DNA (gDNA), viral DNA,bacterial DNA, mtDNA (mitochondrial DNA), ribosomal RNA, cell-free DNA,cell free fetal DNA (cffDNA), mRNA, rRNA, tRNA, nRNA, siRNA, snRNA,snoRNA, scaRNA, microRNA, dsRNA, viral RNA, and the like. In summary,the samples that are used may vary depending on the particularprocessing needs.

Any substance that comprises nucleic acid may be the source of a sample.The substance may be a fluid, e.g., a biological fluid. A fluidicsubstance may include, but not limited to, blood, cord blood, saliva,urine, sweat, serum, semen, vaginal fluid, gastric and digestive fluid,spinal fluid, placental fluid, cavity fluid, ocular fluid, serum, breastmilk, lymphatic fluid, or combinations thereof. The substance may besolid, for example, a biological tissue. The substance may comprisenormal healthy tissues, diseased tissues, or a mix of healthy anddiseased tissues. In some cases, the substance may comprise tumors.Tumors may be benign (non-cancer) or malignant (cancer). Non-limitingexamples of tumors may include: fibrosarcoma, myxo sarcoma, liposarcoma,chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma,endotheliosarcoma, lymphangiosarcoma, lymphangioendothelio sarcoma,synovioma, mesothelioma, Ewing's, leiomyosarcoma, rhabdomyo sarcoma,gastrointestinal system carcinomas, colon carcinoma, pancreatic cancer,breast cancer, genitourinary system carcinomas, ovarian cancer, prostatecancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma,sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma,papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma,bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile ductcarcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor,cervical cancer, endocrine system carcinomas, testicular tumor, lungcarcinoma, small cell lung carcinoma, non-small cell lung carcinoma,bladder carcinoma, epithelial carcinoma, glioma, astrocytoma,medulloblastoma, craniopharyngioma, ependymoma, pinealoma,hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma,melanoma, neuroblastoma, retinoblastoma, or combinations thereof. Thesubstance may be associated with various types of organs. Non-limitingexamples of organs may include brain, liver, lung, kidney, prostate,ovary, spleen, lymph node (including tonsil), thyroid, pancreas, heart,skeletal muscle, intestine, larynx, esophagus, stomach, or combinationsthereof. In some cases, the substance may comprise a variety of cells,including but not limited to: eukaryotic cells, prokaryotic cells, fungicells, heart cells, lung cells, kidney cells, liver cells, pancreascells, reproductive cells, stem cells, induced pluripotent stem cells,gastrointestinal cells, blood cells, cancer cells, bacterial cells,bacterial cells isolated from a human microbiome sample, etc. In somecases, the substance may comprise contents of a cell, such as, forexample, the contents of a single cell or the contents of multiplecells. Methods and systems for analyzing individual cells are providedin, e.g., U.S. Provisional Patent Application No. 62/017,558, filed Jun.26, 2014, the full disclosure of which is hereby incorporated byreference in its entirety.

Samples may be obtained from various subjects. A subject may be a livingsubject or a dead subject. Examples of subjects may include, but notlimited to, humans, mammals, non-human mammals, rodents, amphibians,reptiles, canines, felines, bovines, equines, goats, ovines, hens,avines, mice, rabbits, insects, slugs, microbes, bacteria, parasites, orfish. In some cases, the subject may be a patient who is having,suspected of having, or at a risk of developing a disease or disorder.In some cases, the subject may be a pregnant woman. In some case, thesubject may be a normal healthy pregnant woman. In some cases, thesubject may be a pregnant woman who is at a risking of carrying a babywith certain birth defect.

A sample may be obtained from a subject by various approaches. Forexample, a sample may be obtained from a subject through accessing thecirculatory system (e.g., intravenously or intra-arterially via asyringe or other apparatus), collecting a secreted biological sample(e.g., saliva, sputum urine, feces, etc.), surgically (e.g., biopsy)acquiring a biological sample (e.g., intra-operative samples,post-surgical samples, etc.), swabbing (e.g., buccal swab, oropharyngealswab), or pipetting.

CNVs can be associated with efficacy of a therapy. For example,increased HER2 gene copy number can enhance the response to gefitinibtherapy in advanced non-small cell lung cancer. See Cappuzzo F. et al.(2005) J. Clin. Oncol. 23: 5007-5018. High EGFR gene copy number canpredict for increased sensitivity to lapatinib and capecitabine. SeeFabi et al. (2010) J. Clin. Oncol. 28:15s (2010 ASCO Annual Meeting).High EGFR gene copy number is associated with increased sensitivity tocetuximab and panitumumab.

Copy number variations can be associated with resistance of cancerpatients to certain therapeutics. For example, amplification ofthymidylate synthase can result in resistance to 5-fluorouraciltreatment in metastatic colorectal cancer patients. See Wang et al.(2002) PNAS USA vol. 99, pp. 16156-61.

IX. Computer control systems

The present disclosure provides computer systems that are programmed orotherwise configured to implement methods provided herein, such as, forexample, methods for nucleic sequencing and determination of geneticvariations, storing reference nucleic acid sequences, conductingsequence analysis and/or comparing sample and reference nucleic acidsequences as described herein. An example of such a computer system isshown in FIG. 22. As shown in FIG. 22, the computer system 2201 includesa central processing unit (CPU, also “processor” and “computerprocessor” herein) 2205, which can be a single core or multi coreprocessor, or a plurality of processors for parallel processing. Thecomputer system 2201 also includes memory or memory location 2210 (e.g.,random-access memory, read-only memory, flash memory), electronicstorage unit 2215 (e.g., hard disk), communication interface 2220 (e.g.,network adapter) for communicating with one or more other systems, andperipheral devices 2225, such as cache, other memory, data storageand/or electronic display adapters. The memory 2210, storage unit 2215,interface 2220 and peripheral devices 2225 are in communication with theCPU 2205 through a communication bus (solid lines), such as amotherboard. The storage unit 2215 can be a data storage unit (or datarepository) for storing data. The computer system 2201 can beoperatively coupled to a computer network (“network”) 2230 with the aidof the communication interface 2220. The network 2230 can be theInternet, an internet and/or extranet, or an intranet and/or extranetthat is in communication with the Internet. The network 2230 in somecases is a telecommunication and/or data network. The network 2230 caninclude one or more computer servers, which can enable distributedcomputing, such as cloud computing. The network 2230, in some cases withthe aid of the computer system 2201, can implement a peer-to-peernetwork, which may enable devices coupled to the computer system 2201 tobehave as a client or a server.

The CPU 2205 can execute a sequence of machine-readable instructions,which can be embodied in a program or software. The instructions may bestored in a memory location, such as the memory 2210. Examples ofoperations performed by the CPU 2205 can include fetch, decode, execute,and writeback.

The storage unit 2215 can store files, such as drivers, libraries andsaved programs. The storage unit 2215 can store user data, e.g., userpreferences and user programs. The computer system 2201 in some casescan include one or more additional data storage units that are externalto the computer system 2201, such as located on a remote server that isin communication with the computer system 2201 through an intranet orthe Internet.

The computer system 2201 can communicate with one or more remotecomputer systems through the network 2230. For instance, the computersystem 2201 can communicate with a remote computer system of a user(e.g., operator). Examples of remote computer systems include personalcomputers (e.g., portable PC), slate or tablet PC's (e.g., Apple® iPad,Samsung® Galaxy Tab), telephones, Smart phones (e.g., Apple® iPhone,Android-enabled device, Blackberry®), or personal digital assistants.The user can access the computer system 2201 via the network 2230.

Methods as described herein can be implemented by way of machine (e.g.,computer processor) executable code stored on an electronic storagelocation of the computer system 2201, such as, for example, on thememory 2210 or electronic storage unit 2215. The machine executable ormachine readable code can be provided in the form of software. Duringuse, the code can be executed by the processor 2205. In some cases, thecode can be retrieved from the storage unit 2215 and stored on thememory 2210 for ready access by the processor 2205. In some situations,the electronic storage unit 2215 can be precluded, andmachine-executable instructions are stored on memory 2210.

The code can be pre-compiled and configured for use with a machine havea processer adapted to execute the code, or can be compiled duringruntime. The code can be supplied in a programming language that can beselected to enable the code to execute in a pre-compiled or as-compiledfashion.

Aspects of the systems and methods provided herein, such as the computersystem 2201, can be embodied in programming. Various aspects of thetechnology may be thought of as “products” or “articles of manufacture”typically in the form of machine (or processor) executable code and/orassociated data that is carried on or embodied in a type of machinereadable medium. Machine-executable code can be stored on an electronicstorage unit, such memory (e.g., read-only memory, random-access memory,flash memory) or a hard disk. “Storage” type media can include any orall of the tangible memory of the computers, processors or the like, orassociated modules thereof, such as various semiconductor memories, tapedrives, disk drives and the like, which may provide non-transitorystorage at any time for the software programming. All or portions of thesoftware may at times be communicated through the Internet or variousother telecommunication networks. Such communications, for example, mayenable loading of the software from one computer or processor intoanother, for example, from a management server or host computer into thecomputer platform of an application server. Thus, another type of mediathat may bear the software elements includes optical, electrical andelectromagnetic waves, such as used across physical interfaces betweenlocal devices, through wired and optical landline networks and overvarious air-links. The physical elements that carry such waves, such aswired or wireless links, optical links or the like, also may beconsidered as media bearing the software. As used herein, unlessrestricted to non-transitory, tangible “storage” media, terms such ascomputer or machine “readable medium” refer to any medium thatparticipates in providing instructions to a processor for execution.

Hence, a machine readable medium, such as computer-executable code, maytake many forms, including but not limited to, a tangible storagemedium, a carrier wave medium or physical transmission medium.Non-volatile storage media include, for example, optical or magneticdisks, such as any of the storage devices in any computer(s) or thelike, such as may be used to implement the databases, etc. shown in thedrawings. Volatile storage media include dynamic memory, such as mainmemory of such a computer platform. Tangible transmission media includecoaxial cables; copper wire and fiber optics, including the wires thatcomprise a bus within a computer system. Carrier-wave transmission mediamay take the form of electric or electromagnetic signals, or acoustic orlight waves such as those generated during radio frequency (RF) andinfrared (IR) data communications. Common forms of computer-readablemedia therefore include for example: a floppy disk, a flexible disk,hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD orDVD-ROM, any other optical medium, punch cards paper tape, any otherphysical storage medium with patterns of holes, a RAM, a ROM, a PROM andEPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wavetransporting data or instructions, cables or links transporting such acarrier wave, or any other medium from which a computer may readprogramming code and/or data. Many of these forms of computer readablemedia may be involved in carrying one or more sequences of one or moreinstructions to a processor for execution.

The computer system 2201 can include or be in communication with anelectronic display 2235 that comprises a user interface (UI) forproviding, for example, an output or readout of a nucleic acidsequencing instrument coupled to the computer system 2201. Such readoutcan include a nucleic acid sequencing readout, such as a sequence ofnucleic acid bases that comprise a given nucleic acid sample. The UI mayalso be used to display the results of an analysis making use of suchreadout. Examples of UI's include, without limitation, a graphical userinterface (GUI) and web-based user interface. The electronic display2235 can be a computer monitor, or a capacitive or resistivetouchscreen.

EXAMPLES Example 1: Identification of Phased Variants

Genomic DNA from the NA12878 human cell line was subjected to size basedseparation of fragments using a Blue Pippin DNA sizing system to recoverfragments that were approximately 10 kb in length. The size selectedsample nucleic acids were then copartitioned with barcode beads inaqueous droplets within a fluorinated oil continuous phase using amicrofluidic partitioning system (see e.g., U.S. Provisional PatentApplication No. 61/977,804, filed Apr. 10, 2014, and incorporated hereinby reference in its entirety for all purposes), where the aqueousdroplets also included the dNTPs, thermostable DNA polymerase and otherreagents for carrying out amplification within the droplets, as well asa chemical activator for releasing the barcode oligonucleotides from thebeads. This was repeated both for 1 ng of total input DNA and 2 ng oftotal input DNA. The barcode beads were obtained as a subset of a stocklibrary that represented barcode diversity of over 700,000 differentbarcode sequences. The barcode containing oligonucleotides includedadditional sequence components and had the general structure:

Bead-P5-BC-R1-Nmer

Where P5 and R1 refer to the Illumina attachment and Readl primersequences, respectively, BC denotes the barcode portion of theoligonucleotide, and N-mer denotes a random 10 base N-mer primingsequence used to prime the template nucleic acids. See, e.g., U.S.patent application Ser. No. 14/316,383, filed Jun. 26, 2014, the fulldisclosure of which is hereby incorporated herein by reference in itsentirety for all purposes.

Following bead dissolution, the droplets were thermocycled to allow forprimer extension of the barcode oligos against the template of thesample nucleic acids within each droplet. This resulted in copiedfragments of the sample nucleic acids that included the barcode sequencerepresentative of the originating partition, in addition to the otherincluded sequences set forth above.

After barcode labeling of the copy fragments, the emulsion of dropletsincluding the amplified copy fragments was broken and the additionalsequencer required components, e.g., read2 primer sequence and P7attachment sequence for Illumina sequencer, were added to the copyfragments through additional amplification, which attached thesesequences to the other end of the copy fragments.

The sequencing library was then sequenced on an Illumina HiSeq system at10× coverage, 20× coverage and 30× coverage, and the resulting sequencereads and their associated barcode sequences were then analyzed.Proximally mapping sequences that shared common barcodes were thenassembled into larger contigs, and single nucleotide polymorphisms wereidentified and associated with individual starting molecules based upontheir associated barcodes and sequence mapping, to identify phased SNPs.Sequences that included overlapping phased SNPs were then assembled intophase blocks or inferred contigs of phased sequence data based upon theoverlapping phased SNPs. The resulting data was compared to knownhaplotype maps for the cell line for comparison.

In at least one approach, each allele of a series of heterozygousvariants is assigned to one of two to two haplotypes. A log-likelihoodfunction log P(barcoded reads I phasing assignment, variants) is definedthat returns the log-likelihood of the observed read and barcode data,given a set of variants, and a phasing assignment of the heterozygousvariants. The form of the log-likelihood function derives from two mainobservations about barcoded sequence read data: (1) The reads from onebarcode cover a small fraction of a haploid genome, so the probabilityof one barcode containing reads for both haplotypes in a given region ofthe genome is small. Conversely, the reads for one barcode in a localregion of the genome are very likely to come from a single haplotype;(2) the probability that an observed base differs from the true base inhaplotype it was derived from is described by the Phred QV of theobserved base assigned by the sequencer.

The phasing configuration that maximizes the log-likelihood function,for a given set of barcoded reads and variants is then reported. Themaximum-likelihood scoring haplotype configuration is then found by astructured search procedure. First, a beam search is used to find anoptimal phasing configuration of a small block of neighboring variants(e.g., ˜50 variants). Second the relative phasing of the blocks isdetermined in a sweep over the block junctions. At this point an overallnear-optimal phasing configuration is found and is used as a startingpoint for further optimization. The haplotype assignment of individualvariants is then inverted to find local improvement to the phasing, thedifference in the log-likelihood between the swapped configurationsprovides an estimate of the confidence of that phasing assignment.Finally the phasing configuration is broken into phase blocks that havea high probability of being internally correct. It is then testedwhether to break a phase block at each SNP by comparing thelog-likelihoods of the optimal configuration with a configuration whereall SNPs right of the current SNP have their haplotype assignmentinverted.

The table below, provides the phasing metrics obtained for the NA 12878genome. As is apparent, extremely long phase blocks are obtained fromshort read sequence data, correctly identifying significant percentagesof phased SNPs, with very low short or long switch errors.

10X Coverage 20X Coverage 30X Coverage 30X Beam Search N50 Phase Block 193 kb  385 kb  428 kb  489 kb Longest Phase Block 2121 kb 2514 kb 2514kb 3027 kb Long Switch Error 0.0053 0.0021 0.0018 0.0015 Short SwitchError 0.004 0.0017 0.0014 0.0012 SNPs Phased 83% 94% 95% 95.2%

Further experiments phased SNPs from a number of additional samplesincluding the NA12878 trio (NA12878, NA12882 and NA12877), Gujarati(NA20847), Mexican (NA19662) and African (NA19701) cell line samples.N50 phase block lengths of approximately 1 MB were achieved with greaterthan 95% of the SNPs phased with switch errors of less than 0.3%. Wholeexome sequencing of the same samples, e.g., where targeted pull downfollowed the barcoding, showed genic SNP phasing of approximately 90%again with switch errors of less than 0.3%.

Example 2: Identification of EML-4/ALK Gene Inversions/Translocations

The methods and processes described herein were used to detectstructural variations from a characterized cancer cell line. Inparticular, NCI-H2228 lung cancer cell line is known to have an EML4-ALKfusion translocation within its genome. The structure of the variationcompared to wild type is illustrated in FIG. 15. As shown in the toppanel, in the variant structure, the EML-4 gene, while on the samechromosome, is relatively separate or distant from the ALK gene, isinstead translocated and fused to the ALK gene (See e.g., Choi, et al.,Identification of Novel Isoforms of the EML4-LK Transforming Gene inNon-Small Cell Lung Cancer, J. Cancer Res., 68:4971 (July 2008)). Inconjunction with the translocation, the EML4 gene is also inverted. Thetranslocation is further illustrated in Panel II, as compared to thewild type structure, where the translocation results in the fusion ofexons 1-6 of EML-4 (shown as black boxes) to exons 20-29 of ALK (shownas white boxes), as well as the fusion of exons 7-23 of ALK fused toexons 1-19 of the EML-4.

In order to identify this variation, genomic DNA from the NCI-H2228 cellline was subjected to size separation using a Blue Pippin® system (SageSciences, Inc.), to select for fragments of approximately 10 kb inlength.

The size selected sample nucleic acids were then copartitioned withbarcode beads, amplified and processed into a sequencing library asdescribed above for Example 1, except that the DNA was subjected tohybrid capture using an Agilent SureSelect Exome capture kit afterbarcoding and prior to sequencing. The sequencing library was thensequenced to approximately 80× coverage on an Illumina HiSeq system andthe resulting sequence reads and their associated barcode sequences werethen analyzed. The higher number of shared barcodes among portions ofthe genome that span the translocation event was clearly evident ascompared to the wild type, illustrating structural proximity between thefused components where not present in the wild type. In particular, andas shown in FIG. 16A, the fusion structure showed barcode overlapbetween EML-4 exons 1-6 and ALK exons 20-29, of 12 barcodes, and betweenEML-4 exons 7-23 and ALK exons 1-19, of 20 barcodes, that werecomparable to the overlapping barcodes for the wild type construct forthe heterozygous cell line.

In contrast, a negative control run using a non variant cell line(NA12878) showed substantially only barcode overlap for the wild typevs. the variant construct, as shown in FIG. 16B, with sequence coverageof approximately 140×, and using 3 ng of starting DNA.

In particular, though displaying large numbers of total mapped barcodesto the various sequence segments, only a very small percentage ofoverlapping barcodes, e.g., less than 0.5% of the total mapped barcodedsequences, were seen for the fusion structure by comparison to the wildtype structure which demonstrated very high numbers of common oroverlapping barcodes. As a result, the commonly mapping barcodes acrossfusion or translocation break points provides a powerful basis foridentifying those translocation events.

An algorithm for SV detection was also employed that first searches forall pairs of genomic loci with significant barcode intersection/overlap,encoding this search as an efficient sparse matrix-multiplication.Candidates from this first stage are then filtered utilizing aprobabilistic model that incorporates read-pair, split-read, and barcodedata. SV-calling on NA12878 and NA20847, resulted in calling multiplelarge-scale deletions and inversions and phasing them with respect toadjacent phase blocks, showing consistency of phasing with inheritancepatterns in the nuclear trio descried above.

Example 3: Detecting Increased Susceptibility to Lupus Via CNV Screening

A patient is tested for susceptibility to lupus. Blood is drawn from thepatient. A cell-free DNA sample is sequenced using techniques recitedherein. The sequence is then compared to a known genome referencesequence to determine the CNV of different genes. A low copy number ofFCGR3B (the CD16 cell surface immunoglobulin receptor) indicates anincreased susceptibility to systemic lupus erythematosus. The patient isinformed of any copy number aberrations and the associatedrisks/disease.

Example 4: Detecting Increased Predisposition to Neuroblastoma Via CNVScreening

A patient is tested for predisposition to neuroblastoma. Blood is drawnfrom the patient. A cell-free DNA sample is sequenced using techniquesrecited herein. The sequence is then compared to a known genomereference sequence to determine the CNV of different genes. CNV at1q21.1 indicates an increased predisposition to neuroblastoma. Thepatient is informed of any copy number aberrations and the associatedrisks/disease.

Example 5: Differential Diagnosis of Lung Cancer Via CNV Screening

A patient with chromic cough, weight loss and shortness of breath istested for lung cancer. Blood is drawn from the patient. The circulatingtumor cell (CTC) or cell-free DNA sample is sequenced using techniquesrecited herein. The CTC sequence is then compared to a known genomereference sequence to determine the CNV of different genes. If the EGFRcopy number in the DNA is higher than normal, the patient can bedifferentially diagnosed with non-small cell lung cancer (NSCLC) insteadof small-cell lung cancer. The CTC of non-small cell lung cancer alsohas other copy number variations that may further distinguish it fromsmall-cell lung cancer. Depending on the stage of the cancer, surgery,chemotherapy, or radiation therapy is prescribed.

Small cell lung cancer is most often more rapidly and widely metastaticthan non-small cell lung carcinoma (and hence staged differently).NSCLCs are usually not very sensitive to chemotherapy and/or radiation,so surgery is the treatment of choice if diagnosed at an early stage,often with adjuvant (ancillary) chemotherapy involving cisplatin.Targeted therapy may also be available for patients with non-small celllung cancer (NSCLC), for example ALK inhibitors such as Crizotinib.Targeted therapy blocks the growth of cancer cells by interfering withspecific targeted molecules needed for carcinogenesis and tumor growth,rather than by simply interfering with all rapidly dividing cells (e.g.with traditional chemotherapy).

Example 6: Differential Diagnosis of Fetal Aneuploidies Via Phasing

Fetal aneuploidies are aberrations in chromosome number. Aneuploidiescommonly result in significant physical and neurological impairments. Areduction in the number of X chromosomes is responsible for Turner'ssyndrome. An increase in copy number of chromosome number 21 results inDown's syndrome. Invasive testing such as amniocentesis or ChorionicVillus Sampling (CVS) can lead to risk of pregnancy loss and lessinvasive methods of testing the maternal blood are used here.

A pregnant patient with a family history of Down's syndrome or Turner'ssyndrome is tested. A maternal blood sample containing fetal geneticmaterial is collected. The nucleic acids from different chromosomes arethen separated into different partitions along with barcoded tagmolecules as described herein. The samples are then sequenced and thenumber of each chromosome copies is compared to a sequence on a normaldiploid chromosome. The patient is informed of any copy numberaberrations for different chromosomes and the associated risks/disease.

Example 7: Detecting Chromosomal Translocations Via Phasing forDifferential Diagnosis of Burkitt's Lymphoma

Burkitt's Lymphoma is characterized by a t(8;14) translocation in thechromosomes. A patient generally diagnosed with lymphoma is tested forBurkitt's Lymphoma. A tumor-biopsy specimen is collected from the lymphnode. The nucleic acids from different chromosomes are the separatedinto different partitions along with barcoded tag molecules as describedherein. The samples are then sequenced and compared to a control DNAsample to detect chromosomal translocation. If the patient is diagnosedas having Burkitt's Lymphoma, a more intensive chemotherapy regimen,including the CHOP or R-CHOP regimen, can be required than with othertypes of lymphoma. CHOP consists of: Cyclophosphamide, an alkylatingagent which damages DNA by binding to it and causing the formation ofcross-links; Hydroxydaunorubicin (also called doxorubicin orAdriamycin), an intercalating agent which damages DNA by insertingitself between DNA bases; Oncovin (vincristine), which prevents cellsfrom duplicating by binding to the protein tubulin; Prednisone orprednisolone, which are corticosteroids. This regimen can also becombined with the monoclonal antibody rituximab since Burkitt's thelymphoma is of B cell origin; this combination is called R-CHOP.

Example 8: Phasing a Fetal Genome Sequence Derived from Cell-Free DNA byComparison to Parental Genomes

A sample comprising maternal DNA from a pregnant patient and a samplecomprising paternal DNA from the father of the fetus are collected. Thenucleic acids from each sample are separated into different partitionsalong with molecular barcoded tags as described herein. The samples arethen sequenced and the sequences are used to generate inferred contigsfor each of the partitioned maternal and paternal fragments. Theinferred contigs are used to construct haplotype blocks for portions ofeach of the maternal and paternal chromosomes.

A maternal blood sample containing fetal genetic material is collected.The cell-free DNA is sequenced to generate a sequences of both thematernal circulating DNA and the fetal circulating DNA. The reads arecompared to the paternal and maternal phase blocks generated above. Somephase blocks have undergone recombination during meiosis. The fetalmaterial is identified that matches the paternal phase blocks and notthe maternal phase blocks. In some cases, the fetal material matches theentirety of a paternal phase block and it is determined that the fetushas that paternal phase block in the paternally inherited chromosome. Inother cases, the fetal material matches part of a phase block and thenmatches a second phase block, where the two phase blocks are onhomologous chromosomal regions in the paternal genome. It is determinedthat a meiotic recombination event occurred at this region, the mostlikely point of recombination is determined, and a novel fetal phaseblock that is a combination of two paternal phase blocks is produced.

The sequences of the circulating DNA are compared to the maternal phaseblocks. Sites of heterozygosity in the maternal phase blocks are used todetermine the most likely phase of the maternally derived fetalchromosomes. The circulating DNA sequences are used to determine thecopy number at the heterozygous sites of the maternal genome. Elevatedcopy numbers of specific maternal phase blocks indicates that thematernally derived chromosome of the fetus contains the sequence of theelevated phase block. In some cases, similarly to that described in thepaternal case, at first one phase block of a homologous region willappear elevated, and then a portion of another phase block of the sameregion will appear elevated, indicating that meiotic recombination hasoccurred. In these cases, a the most likely region of recombination isdetermined and a new fetal phase block is constructed from the twomaternal phase blocks.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. It is not intendedthat the invention be limited by the specific examples provided withinthe specification. While the invention has been described with referenceto the aforementioned specification, the descriptions and illustrationsof the embodiments herein are not meant to be construed in a limitingsense. Numerous variations, changes, and substitutions will now occur tothose skilled in the art without departing from the invention.Furthermore, it shall be understood that all aspects of the inventionare not limited to the specific depictions, configurations or relativeproportions set forth herein which depend upon a variety of conditionsand variables. It should be understood that various alternatives to theembodiments of the invention described herein may be employed inpracticing the invention. It is therefore contemplated that theinvention shall also cover any such alternatives, modifications,variations or equivalents. It is intended that the following claimsdefine the scope of the invention and that methods and structures withinthe scope of these claims and their equivalents be covered thereby.

1. A method for nucleic acid analysis, comprising: (a) generating aplurality of barcoded parental nucleic acid molecules in a plurality ofpartitions using (i) parental nucleic acid molecules derived from aparental biological sample and (ii) nucleic acid barcode molecules froma plurality of nucleic acid barcode molecules; (b) removing or releasingsaid plurality of barcoded parental nucleic acid molecules from saidplurality of partitions; (c) using said barcoded parental nucleic acidmolecules or derivatives thereof to generate parental nucleic acidsequence information comprising one or more nucleic acid sequences ofsaid plurality of parental nucleic acid molecules; and (d) processingfetal nucleic acid sequence information from one or more fetal nucleicacid molecules against said parental nucleic acid sequence informationto identify one or more variations in said one or more fetal nucleicacid molecules.
 2. The method of claim 1, further comprising, prior to(a), generating a plurality of partitions comprising (i) a plurality ofparental nucleic acid molecules derived from said parental biologicalsample; and (ii) said plurality of nucleic acid barcode molecules. 3.The method of claim 1, wherein in (c), said parental nucleic acidsequence information is generated by sequencing said barcoded parentalnucleic acid molecules or derivatives thereof.
 4. The method of claim 1,wherein, in (c), said parental nucleic acid sequence informationcomprises haplotype blocks, and wherein (d) comprises processing saidfetal nucleic acid sequence information against at least a subset ofsaid haplotype blocks.
 5. The method of claim 1, further comprisingobtaining, from a subject having a fetus, a maternal biological sample,and deriving from said maternal biological sample (i) said parentalnucleic acid molecules; and (ii) fetal nucleic acid molecules of saidfetus.
 6. The method of claim 5, wherein said fetal nucleic acidmolecules are derived from a cell-free portion of said maternalbiological sample.
 7. The method of claim 5, further comprisingsequencing said fetal nucleic acid molecules or derivatives thereof togenerate said fetal nucleic acid sequence information.
 8. The method ofclaim 5, wherein said maternal biological sample is a blood sample fromsaid subject.
 9. The method of claim 1, wherein said one or more fetalnucleic acid molecules are from a fetus, and wherein said one or morefetal nucleic acid molecules are derived from a cell-free biologicalsample of a subject having said fetus.
 10. The method of claim 9,wherein said cell-free biological sample is obtained from a bodily fluidof said subject.
 11. The method of claim 10, wherein said bodily fluidis blood.
 12. The method of claim 10, wherein said bodily fluid isserum.
 13. The method of claim 1, further comprising enriching said oneor more fetal nucleic acid molecules or derivatives thereof from a fetalsample.
 14. The method of claim 1, wherein in (a) said parental nucleicacid molecules are derived from a maternal biological sample, andwherein, in (d), said parental nucleic acid sequence informationcomprises said one or more nucleic acid sequences derived from saidmaternal biological sample.
 15. The method of claim 14, wherein saidparental nucleic acid sequence information further comprises one or morenucleic acid sequences derived from a paternal biological sample. 16.The method of claim 1, wherein said plurality of partitions is aplurality of droplets.
 17. The method of claim 1, wherein said pluralityof partitions is a plurality of wells.
 18. The method of claim 1,wherein said one or more variations comprise a copy number variation, aninsertion, a deletion, a translocation, an inversion, a retrotransposon,a rearrangement, a repeat expansion, a duplication, a gene fusion, asingle nucleotide polymorphisms, or any combination thereof.
 19. Themethod of claim 1, wherein said a given partition of said plurality ofpartitions comprises a parental nucleic acid molecule, wherein saidparental nucleic acid molecule has a length longer than 1 kb.
 20. Themethod of claim 19, wherein said parental nucleic acid molecule has alength longer than 10 kb.
 21. The method of claim 1, wherein saidplurality of partitions further comprise a plurality of beads, wherein abead of said plurality of beads comprises a plurality of nucleic acidbarcode molecules attached thereto, wherein a partition of saidplurality of partitions comprises said bead.
 22. The method of claim 21,wherein said bead comprises a plurality of nucleic acid barcodemolecules comprising a common barcode sequence.
 23. The method of claim22, wherein said common barcode sequence is different from commonbarcode sequences of other beads of said plurality of beads.
 24. Themethod of claim 21, wherein said plurality of beads is a plurality ofgel beads.
 25. The method of claim 21, wherein said plurality of nucleicacid barcode molecules is releasably attached to said bead.
 26. Themethod of claim 25, wherein said plurality of nucleic acid barcodemolecules is released upon application of a chemical stimulus.
 27. Themethod of claim 26, wherein said chemical stimulus is a reducing agent.28. The method of claim 26, wherein said partition further comprisessaid chemical stimulus.
 29. The method of claim 25, wherein saidplurality of nucleic acid barcode molecules is released upon applicationof a thermal stimulus.
 30. The method of claim 25, wherein saidplurality of nucleic acid barcode molecules is released upon applicationof a photo-stimulus.